diff --git a/docs/content/en/docs/documentation/eventing.md b/docs/content/en/docs/documentation/eventing.md
index 06b8ccf9e9..d2a104737b 100644
--- a/docs/content/en/docs/documentation/eventing.md
+++ b/docs/content/en/docs/documentation/eventing.md
@@ -139,6 +139,14 @@ rare corner cases. Returning an empty set means that the mapper considered the s
 resource event as irrelevant and the SDK will thus not trigger a reconciliation of the primary
 resource in that situation.
 
+On an update event, the SDK calls `toPrimaryResourceIDs` for **both the old and the new version**
+of the secondary resource. This way it can reconcile not only the primaries that the secondary
+currently maps to, but also those it previously mapped to and no longer does. So when a reference
+changes — including when only a subset of the referenced primaries changes — both the newly
+referenced and the dropped primaries are reconciled, and a dropped primary can revert to its
+default state. Because the mapper can be invoked for an older version of a resource, keep your
+implementation a pure function of the resource passed to it.
+
 Adding a `SecondaryToPrimaryMapper` is typically sufficient when there is a one-to-many relationship
 between primary and secondary resources. The secondary resources can be mapped to its primary
 owner, and this is enough information to also get these secondary resources from the `Context`
diff --git a/operator-framework-core/src/main/java/io/javaoperatorsdk/operator/processing/event/source/SecondaryToPrimaryMapper.java b/operator-framework-core/src/main/java/io/javaoperatorsdk/operator/processing/event/source/SecondaryToPrimaryMapper.java
index 0c6126105c..d1f79a7981 100644
--- a/operator-framework-core/src/main/java/io/javaoperatorsdk/operator/processing/event/source/SecondaryToPrimaryMapper.java
+++ b/operator-framework-core/src/main/java/io/javaoperatorsdk/operator/processing/event/source/SecondaryToPrimaryMapper.java
@@ -26,9 +26,15 @@
  */
 @FunctionalInterface
 public interface SecondaryToPrimaryMapper<R> {
+
   /**
-   * @param resource - secondary
-   * @return set of primary resource IDs
+   * Maps a secondary resource to the set of primary resources that should be reconciled in
+   * response.
+   *
+   * @param resource the secondary resource for which an event was received
+   * @return set of primary resource IDs to enqueue for reconciliation; an empty set means the event
+   *     is irrelevant and no reconciliation is triggered. On update events, this method is invoked
+   *     for both the old and the new versions of the resource.
    */
   Set<ResourceID> toPrimaryResourceIDs(R resource);
 }
diff --git a/operator-framework-core/src/main/java/io/javaoperatorsdk/operator/processing/event/source/informer/DefaultPrimaryToSecondaryIndex.java b/operator-framework-core/src/main/java/io/javaoperatorsdk/operator/processing/event/source/informer/DefaultPrimaryToSecondaryIndex.java
index 2b4f3814b3..2ec8aa9372 100644
--- a/operator-framework-core/src/main/java/io/javaoperatorsdk/operator/processing/event/source/informer/DefaultPrimaryToSecondaryIndex.java
+++ b/operator-framework-core/src/main/java/io/javaoperatorsdk/operator/processing/event/source/informer/DefaultPrimaryToSecondaryIndex.java
@@ -32,18 +32,42 @@ public DefaultPrimaryToSecondaryIndex(SecondaryToPrimaryMapper<R> secondaryToPri
   }
 
   @Override
-  public synchronized void onAddOrUpdate(R resource) {
+  public synchronized Set<ResourceID> onAddOrUpdate(R resource, R oldResource) {
+
     Set<ResourceID> primaryResources = secondaryToPrimaryMapper.toPrimaryResourceIDs(resource);
+
+    var secondaryId = ResourceID.fromResource(resource);
+
     primaryResources.forEach(
         primaryResource -> {
           var resourceSet =
               index.computeIfAbsent(primaryResource, pr -> ConcurrentHashMap.newKeySet());
-          resourceSet.add(ResourceID.fromResource(resource));
+          resourceSet.add(secondaryId);
         });
+
+    if (oldResource != null) {
+      var obsoletePrimaries =
+          new HashSet<>(secondaryToPrimaryMapper.toPrimaryResourceIDs(oldResource));
+      if (!primaryResources.containsAll(obsoletePrimaries)) {
+        var result = new HashSet<>(primaryResources);
+        obsoletePrimaries.removeAll(primaryResources);
+        obsoletePrimaries.forEach(
+            p ->
+                index.computeIfPresent(
+                    p,
+                    (id, currentSet) -> {
+                      currentSet.remove(secondaryId);
+                      return currentSet.isEmpty() ? null : currentSet;
+                    }));
+        result.addAll(obsoletePrimaries);
+        return result;
+      }
+    }
+    return primaryResources;
   }
 
   @Override
-  public synchronized void onDelete(R resource) {
+  public synchronized Set<ResourceID> onDelete(R resource) {
     Set<ResourceID> primaryResources = secondaryToPrimaryMapper.toPrimaryResourceIDs(resource);
     primaryResources.forEach(
         primaryResource -> {
@@ -58,6 +82,7 @@ public synchronized void onDelete(R resource) {
             }
           }
         });
+    return primaryResources;
   }
 
   @Override
diff --git a/operator-framework-core/src/main/java/io/javaoperatorsdk/operator/processing/event/source/informer/InformerEventSource.java b/operator-framework-core/src/main/java/io/javaoperatorsdk/operator/processing/event/source/informer/InformerEventSource.java
index c425a4d413..30fd6a7fb5 100644
--- a/operator-framework-core/src/main/java/io/javaoperatorsdk/operator/processing/event/source/informer/InformerEventSource.java
+++ b/operator-framework-core/src/main/java/io/javaoperatorsdk/operator/processing/event/source/informer/InformerEventSource.java
@@ -15,6 +15,7 @@
  */
 package io.javaoperatorsdk.operator.processing.event.source.informer;
 
+import java.util.HashSet;
 import java.util.Optional;
 import java.util.Set;
 import java.util.stream.Collectors;
@@ -127,10 +128,10 @@ public synchronized void onDelete(R resource, boolean deletedFinalStateUnknown)
           if (resultEvent.isEmpty()) {
             return;
           }
-          primaryToSecondaryIndex.onDelete(resource);
+          var primaryIds = primaryToSecondaryIndex.onDelete(resource);
           if (eventAcceptedByFilter(
               ResourceAction.DELETED, resource, null, deletedFinalStateUnknown)) {
-            propagateEvent(resource);
+            propagateEvent(resource, null, primaryIds);
           }
         });
   }
@@ -144,11 +145,12 @@ protected void handleEvent(
     // onAdd/onUpdate/onDelete watch paths. The index is updated for DELETED regardless of the
     // filter outcome — the resource is really gone, so leaving a tombstone in the index would
     // make getSecondaryResources keep returning a stale entry.
+    Set<ResourceID> primaryIds = null;
     if (action == ResourceAction.DELETED) {
       log.debug(
           "handleEvent: removing from primaryToSecondaryIndex. id={}",
           ResourceID.fromResource(resource));
-      primaryToSecondaryIndex.onDelete(resource);
+      primaryIds = primaryToSecondaryIndex.onDelete(resource);
     }
     if (!eventAcceptedByFilter(action, resource, oldResource, deletedFinalStateUnknown)) {
       if (log.isDebugEnabled()) {
@@ -166,7 +168,7 @@ protected void handleEvent(
           action,
           resource.getMetadata().getResourceVersion());
     }
-    propagateEvent(resource);
+    propagateEvent(resource, oldResource, primaryIds);
   }
 
   @Override
@@ -177,12 +179,12 @@ public synchronized void start() {
     super.start();
     // this makes sure that on first reconciliation all resources are
     // present on the index
-    manager().list().forEach(primaryToSecondaryIndex::onAddOrUpdate);
+    manager().list().forEach(r -> primaryToSecondaryIndex.onAddOrUpdate(r, null));
   }
 
   @SuppressWarnings("unchecked")
   private synchronized void onAddOrUpdate(ResourceAction action, R newObject, R oldObject) {
-    primaryToSecondaryIndex.onAddOrUpdate(newObject);
+    var primaryIds = primaryToSecondaryIndex.onAddOrUpdate(newObject, oldObject);
     var resourceID = ResourceID.fromResource(newObject);
 
     var resultEvent = temporaryResourceCache.onAddOrUpdateEvent(action, newObject, oldObject);
@@ -194,15 +196,22 @@ private synchronized void onAddOrUpdate(ResourceAction action, R newObject, R ol
           "Propagating event for {}, resource with same version not result of a our update.",
           action);
       var event = resultEvent.get();
-      propagateEvent((R) event.getResource().orElseThrow());
+      propagateEvent((R) event.getResource().orElseThrow(), oldObject, primaryIds);
     } else {
       log.debug("Event filtered out for operation: {}, resourceID: {}", action, resourceID);
     }
   }
 
-  protected void propagateEvent(R object) {
-    var primaryResourceIdSet =
-        configuration().getSecondaryToPrimaryMapper().toPrimaryResourceIDs(object);
+  protected void propagateEvent(R resource, R oldResource, Set<ResourceID> primaryResourceIdSet) {
+    if (primaryResourceIdSet == null) {
+      primaryResourceIdSet = new HashSet<>();
+      primaryResourceIdSet.addAll(
+          configuration().getSecondaryToPrimaryMapper().toPrimaryResourceIDs(resource));
+      if (oldResource != null) {
+        primaryResourceIdSet.addAll(
+            configuration().getSecondaryToPrimaryMapper().toPrimaryResourceIDs(oldResource));
+      }
+    }
     if (primaryResourceIdSet.isEmpty()) {
       return;
     }
@@ -249,16 +258,16 @@ public Set<R> getSecondaryResources(P primary) {
   @Override
   public void handleRecentResourceUpdate(
       ResourceID resourceID, R resource, R previousVersionOfResource) {
-    handleRecentCreateOrUpdate(resource);
+    handleRecentCreateOrUpdate(resource, previousVersionOfResource);
   }
 
   @Override
   public void handleRecentResourceCreate(ResourceID resourceID, R resource) {
-    handleRecentCreateOrUpdate(resource);
+    handleRecentCreateOrUpdate(resource, null);
   }
 
-  private void handleRecentCreateOrUpdate(R newResource) {
-    primaryToSecondaryIndex.onAddOrUpdate(newResource);
+  private void handleRecentCreateOrUpdate(R newResource, R previousVersion) {
+    primaryToSecondaryIndex.onAddOrUpdate(newResource, previousVersion);
     temporaryResourceCache.putResource(newResource);
   }
 
diff --git a/operator-framework-core/src/main/java/io/javaoperatorsdk/operator/processing/event/source/informer/NOOPPrimaryToSecondaryIndex.java b/operator-framework-core/src/main/java/io/javaoperatorsdk/operator/processing/event/source/informer/NOOPPrimaryToSecondaryIndex.java
index ce217a5543..b22b958fc2 100644
--- a/operator-framework-core/src/main/java/io/javaoperatorsdk/operator/processing/event/source/informer/NOOPPrimaryToSecondaryIndex.java
+++ b/operator-framework-core/src/main/java/io/javaoperatorsdk/operator/processing/event/source/informer/NOOPPrimaryToSecondaryIndex.java
@@ -33,13 +33,14 @@ public static <T extends HasMetadata> NOOPPrimaryToSecondaryIndex<T> getInstance
   private NOOPPrimaryToSecondaryIndex() {}
 
   @Override
-  public void onAddOrUpdate(R resource) {
-    // empty method because of noop implementation
+  public Set<ResourceID> onAddOrUpdate(R resource, R oldResource) {
+    return null;
   }
 
   @Override
-  public void onDelete(R resource) {
+  public Set<ResourceID> onDelete(R resource) {
     // empty method because of noop implementation
+    return null;
   }
 
   @Override
diff --git a/operator-framework-core/src/main/java/io/javaoperatorsdk/operator/processing/event/source/informer/PrimaryToSecondaryIndex.java b/operator-framework-core/src/main/java/io/javaoperatorsdk/operator/processing/event/source/informer/PrimaryToSecondaryIndex.java
index f88e481316..65fd692b25 100644
--- a/operator-framework-core/src/main/java/io/javaoperatorsdk/operator/processing/event/source/informer/PrimaryToSecondaryIndex.java
+++ b/operator-framework-core/src/main/java/io/javaoperatorsdk/operator/processing/event/source/informer/PrimaryToSecondaryIndex.java
@@ -22,9 +22,9 @@
 
 public interface PrimaryToSecondaryIndex<R extends HasMetadata> {
 
-  void onAddOrUpdate(R resource);
+  Set<ResourceID> onAddOrUpdate(R resource, R oldResource);
 
-  void onDelete(R resource);
+  Set<ResourceID> onDelete(R resource);
 
   Set<ResourceID> getSecondaryResources(ResourceID primary);
 }
diff --git a/operator-framework-core/src/test/java/io/javaoperatorsdk/operator/processing/event/source/informer/InformerEventSourceTest.java b/operator-framework-core/src/test/java/io/javaoperatorsdk/operator/processing/event/source/informer/InformerEventSourceTest.java
index dda08a7c98..3d9e8cbc1d 100644
--- a/operator-framework-core/src/test/java/io/javaoperatorsdk/operator/processing/event/source/informer/InformerEventSourceTest.java
+++ b/operator-framework-core/src/test/java/io/javaoperatorsdk/operator/processing/event/source/informer/InformerEventSourceTest.java
@@ -655,11 +655,13 @@ void handleEventUpdatesIndexWhenDeletePropagatesFromTempCache() throws Exception
     // and getSecondaryResources keeps returning a tombstone.
     var indexMock = injectIndexMock();
     var resource = testDeployment();
+    // onDelete now returns the primaries to reconcile; propagateEvent uses that set directly
+    when(indexMock.onDelete(resource)).thenReturn(Set.of(ResourceID.fromResource(resource)));
 
     informerEventSource.handleEvent(ResourceAction.DELETED, resource, null, false);
 
     verify(indexMock, times(1)).onDelete(resource);
-    verify(indexMock, never()).onAddOrUpdate(any());
+    verify(indexMock, never()).onAddOrUpdate(any(), any());
     verify(eventHandlerMock, times(1)).handleEvent(any());
   }
 
@@ -673,7 +675,7 @@ void handleEventDoesNotTouchIndexForNonDeleteAction() throws Exception {
         ResourceAction.UPDATED, testDeployment(), testDeployment(), null);
 
     verify(indexMock, never()).onDelete(any());
-    verify(indexMock, never()).onAddOrUpdate(any());
+    verify(indexMock, never()).onAddOrUpdate(any(), any());
     verify(eventHandlerMock, times(1)).handleEvent(any());
   }
 
@@ -745,14 +747,17 @@ private void assertNoEventProduced() {
     await()
         .pollDelay(Duration.ofMillis(70))
         .timeout(Duration.ofMillis(150))
-        .untilAsserted(() -> verify(informerEventSource, never()).propagateEvent(any()));
+        .untilAsserted(
+            () -> verify(informerEventSource, never()).propagateEvent(any(), any(), any()));
   }
 
   private void expectPropagateEvent(Deployment newResourceVersion) {
     await()
         .atMost(Duration.ofSeconds(1))
         .untilAsserted(
-            () -> verify(informerEventSource, times(1)).propagateEvent(newResourceVersion));
+            () ->
+                verify(informerEventSource, times(1))
+                    .propagateEvent(eq(newResourceVersion), any(), any()));
   }
 
   private void expectHandleUpdateEvent(int newResourceVersion, int oldResourceVersion) {
diff --git a/operator-framework-core/src/test/java/io/javaoperatorsdk/operator/processing/event/source/informer/PrimaryToSecondaryIndexTest.java b/operator-framework-core/src/test/java/io/javaoperatorsdk/operator/processing/event/source/informer/PrimaryToSecondaryIndexTest.java
index 91bca3708c..d298bce8bb 100644
--- a/operator-framework-core/src/test/java/io/javaoperatorsdk/operator/processing/event/source/informer/PrimaryToSecondaryIndexTest.java
+++ b/operator-framework-core/src/test/java/io/javaoperatorsdk/operator/processing/event/source/informer/PrimaryToSecondaryIndexTest.java
@@ -15,6 +15,7 @@
  */
 package io.javaoperatorsdk.operator.processing.event.source.informer;
 
+import java.util.Map;
 import java.util.Set;
 
 import org.junit.jupiter.api.BeforeEach;
@@ -27,6 +28,7 @@
 
 import static org.assertj.core.api.Assertions.assertThat;
 import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.ArgumentMatchers.eq;
 import static org.mockito.Mockito.mock;
 import static org.mockito.Mockito.when;
 
@@ -58,7 +60,7 @@ void returnsEmptySetOnEmptyIndex() {
 
   @Test
   void indexesNewResources() {
-    primaryToSecondaryIndex.onAddOrUpdate(secondary1);
+    primaryToSecondaryIndex.onAddOrUpdate(secondary1, null);
 
     var secondaryResources1 = primaryToSecondaryIndex.getSecondaryResources(primaryID1);
     var secondaryResources2 = primaryToSecondaryIndex.getSecondaryResources(primaryID2);
@@ -69,8 +71,8 @@ void indexesNewResources() {
 
   @Test
   void indexesAdditionalResources() {
-    primaryToSecondaryIndex.onAddOrUpdate(secondary1);
-    primaryToSecondaryIndex.onAddOrUpdate(secondary2);
+    primaryToSecondaryIndex.onAddOrUpdate(secondary1, null);
+    primaryToSecondaryIndex.onAddOrUpdate(secondary2, null);
 
     var secondaryResources1 = primaryToSecondaryIndex.getSecondaryResources(primaryID1);
     var secondaryResources2 = primaryToSecondaryIndex.getSecondaryResources(primaryID2);
@@ -83,8 +85,8 @@ void indexesAdditionalResources() {
 
   @Test
   void removingResourceFromIndex() {
-    primaryToSecondaryIndex.onAddOrUpdate(secondary1);
-    primaryToSecondaryIndex.onAddOrUpdate(secondary2);
+    primaryToSecondaryIndex.onAddOrUpdate(secondary1, null);
+    primaryToSecondaryIndex.onAddOrUpdate(secondary2, null);
     primaryToSecondaryIndex.onDelete(secondary1);
 
     var secondaryResources1 = primaryToSecondaryIndex.getSecondaryResources(primaryID1);
@@ -102,6 +104,74 @@ void removingResourceFromIndex() {
     assertThat(secondaryResources2).isEmpty();
   }
 
+  @Test
+  void updateRemovesObsoletePrimaryWhenReferenceNarrows() {
+    // initial version references both primaries (default stub)
+    primaryToSecondaryIndex.onAddOrUpdate(secondary1, null);
+
+    // updated version references only primaryID1
+    var updated = updatedVersionOf("secondary1");
+    when(secondaryToPrimaryMapperMock.toPrimaryResourceIDs(eq(updated)))
+        .thenReturn(Set.of(primaryID1));
+    primaryToSecondaryIndex.onAddOrUpdate(updated, secondary1);
+
+    assertThat(primaryToSecondaryIndex.getSecondaryResources(primaryID1))
+        .containsOnly(ResourceID.fromResource(secondary1));
+    // primaryID2 is no longer referenced, so its (now empty) entry is removed
+    assertThat(primaryToSecondaryIndex.getSecondaryResources(primaryID2)).isEmpty();
+  }
+
+  @Test
+  void updateMovesSecondaryBetweenPrimaries() {
+    // initial version references only primaryID1
+    when(secondaryToPrimaryMapperMock.toPrimaryResourceIDs(eq(secondary1)))
+        .thenReturn(Set.of(primaryID1));
+    primaryToSecondaryIndex.onAddOrUpdate(secondary1, null);
+
+    // updated version moves the reference to primaryID2
+    var updated = updatedVersionOf("secondary1");
+    when(secondaryToPrimaryMapperMock.toPrimaryResourceIDs(eq(updated)))
+        .thenReturn(Set.of(primaryID2));
+    primaryToSecondaryIndex.onAddOrUpdate(updated, secondary1);
+
+    assertThat(primaryToSecondaryIndex.getSecondaryResources(primaryID1)).isEmpty();
+    assertThat(primaryToSecondaryIndex.getSecondaryResources(primaryID2))
+        .containsOnly(ResourceID.fromResource(secondary1));
+  }
+
+  @Test
+  void updateOnlyRemovesUpdatedSecondaryFromObsoletePrimary() {
+    // two secondaries, each referencing both primaries (default stub)
+    primaryToSecondaryIndex.onAddOrUpdate(secondary1, null);
+    primaryToSecondaryIndex.onAddOrUpdate(secondary2, null);
+
+    // secondary1 stops referencing primaryID2
+    var updated = updatedVersionOf("secondary1");
+    when(secondaryToPrimaryMapperMock.toPrimaryResourceIDs(eq(updated)))
+        .thenReturn(Set.of(primaryID1));
+    primaryToSecondaryIndex.onAddOrUpdate(updated, secondary1);
+
+    assertThat(primaryToSecondaryIndex.getSecondaryResources(primaryID1))
+        .containsOnly(ResourceID.fromResource(secondary1), ResourceID.fromResource(secondary2));
+    // primaryID2 is still referenced by secondary2, so only secondary1 is removed from it
+    assertThat(primaryToSecondaryIndex.getSecondaryResources(primaryID2))
+        .containsOnly(ResourceID.fromResource(secondary2));
+  }
+
+  @Test
+  void updateKeepsIndexUnchangedWhenReferencedPrimariesDoNotChange() {
+    primaryToSecondaryIndex.onAddOrUpdate(secondary1, null);
+
+    // updated version still references both primaries (default stub applies to it as well)
+    var updated = updatedVersionOf("secondary1");
+    primaryToSecondaryIndex.onAddOrUpdate(updated, secondary1);
+
+    assertThat(primaryToSecondaryIndex.getSecondaryResources(primaryID1))
+        .containsOnly(ResourceID.fromResource(secondary1));
+    assertThat(primaryToSecondaryIndex.getSecondaryResources(primaryID2))
+        .containsOnly(ResourceID.fromResource(secondary1));
+  }
+
   ConfigMap secondary(String name) {
     ConfigMap configMap = new ConfigMap();
     configMap.setMetadata(new ObjectMeta());
@@ -109,4 +179,14 @@ ConfigMap secondary(String name) {
     configMap.getMetadata().setNamespace("default");
     return configMap;
   }
+
+  /**
+   * Returns a new version of a secondary with the same {@link ResourceID} but a different content,
+   * so it represents an updated resource that the mapper mock can be stubbed for independently.
+   */
+  ConfigMap updatedVersionOf(String name) {
+    ConfigMap configMap = secondary(name);
+    configMap.getMetadata().setLabels(Map.of("version", "updated"));
+    return configMap;
+  }
 }
diff --git a/operator-framework/src/test/java/io/javaoperatorsdk/operator/baseapi/secondarytoprimaryreferencechange/ConfigCustomResource.java b/operator-framework/src/test/java/io/javaoperatorsdk/operator/baseapi/secondarytoprimaryreferencechange/ConfigCustomResource.java
new file mode 100644
index 0000000000..f598017c4c
--- /dev/null
+++ b/operator-framework/src/test/java/io/javaoperatorsdk/operator/baseapi/secondarytoprimaryreferencechange/ConfigCustomResource.java
@@ -0,0 +1,33 @@
+/*
+ * Copyright Java Operator SDK Authors
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *         http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package io.javaoperatorsdk.operator.baseapi.secondarytoprimaryreferencechange;
+
+import io.fabric8.kubernetes.api.model.Namespaced;
+import io.fabric8.kubernetes.client.CustomResource;
+import io.fabric8.kubernetes.model.annotation.Group;
+import io.fabric8.kubernetes.model.annotation.Kind;
+import io.fabric8.kubernetes.model.annotation.ShortNames;
+import io.fabric8.kubernetes.model.annotation.Version;
+
+/**
+ * Secondary resource that references one or more {@link TargetCustomResource}s via {@code
+ * spec.targetNames} and serves as input for them.
+ */
+@Group("sample.javaoperatorsdk")
+@Version("v1")
+@Kind("SecondaryToPrimaryRefConfig")
+@ShortNames("s2pconfig")
+public class ConfigCustomResource extends CustomResource<ConfigSpec, Void> implements Namespaced {}
diff --git a/operator-framework/src/test/java/io/javaoperatorsdk/operator/baseapi/secondarytoprimaryreferencechange/ConfigSpec.java b/operator-framework/src/test/java/io/javaoperatorsdk/operator/baseapi/secondarytoprimaryreferencechange/ConfigSpec.java
new file mode 100644
index 0000000000..9d2e5139e6
--- /dev/null
+++ b/operator-framework/src/test/java/io/javaoperatorsdk/operator/baseapi/secondarytoprimaryreferencechange/ConfigSpec.java
@@ -0,0 +1,48 @@
+/*
+ * Copyright Java Operator SDK Authors
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *         http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package io.javaoperatorsdk.operator.baseapi.secondarytoprimaryreferencechange;
+
+import java.util.List;
+
+public class ConfigSpec {
+
+  /**
+   * Names of the {@link TargetCustomResource}s (in the same namespace) this config provides input
+   * for. A single config can reference multiple targets.
+   */
+  private List<String> targetNames;
+
+  /** Value to be applied to the referenced targets' status. */
+  private String value;
+
+  public List<String> getTargetNames() {
+    return targetNames;
+  }
+
+  public ConfigSpec setTargetNames(List<String> targetNames) {
+    this.targetNames = targetNames;
+    return this;
+  }
+
+  public String getValue() {
+    return value;
+  }
+
+  public ConfigSpec setValue(String value) {
+    this.value = value;
+    return this;
+  }
+}
diff --git a/operator-framework/src/test/java/io/javaoperatorsdk/operator/baseapi/secondarytoprimaryreferencechange/ConfigToTargetMapper.java b/operator-framework/src/test/java/io/javaoperatorsdk/operator/baseapi/secondarytoprimaryreferencechange/ConfigToTargetMapper.java
new file mode 100644
index 0000000000..72930261de
--- /dev/null
+++ b/operator-framework/src/test/java/io/javaoperatorsdk/operator/baseapi/secondarytoprimaryreferencechange/ConfigToTargetMapper.java
@@ -0,0 +1,48 @@
+/*
+ * Copyright Java Operator SDK Authors
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *         http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package io.javaoperatorsdk.operator.baseapi.secondarytoprimaryreferencechange;
+
+import java.util.Set;
+import java.util.stream.Collectors;
+
+import io.javaoperatorsdk.operator.processing.event.ResourceID;
+import io.javaoperatorsdk.operator.processing.event.source.SecondaryToPrimaryMapper;
+
+/**
+ * Maps a {@link ConfigCustomResource} (secondary) to the {@link TargetCustomResource}s (primaries)
+ * it references via {@code spec.targetNames}. A config can reference multiple targets.
+ *
+ * <p>The mapper only reports the <em>current</em> references. When the referenced set changes — for
+ * example when a subset of the targets is replaced — the framework's primary-to-secondary index
+ * reconciles both the newly referenced targets and the ones that are no longer referenced, so a
+ * dropped target reverts to its default value. The mapper therefore does not need to know about the
+ * previous version of the resource.
+ */
+public class ConfigToTargetMapper implements SecondaryToPrimaryMapper<ConfigCustomResource> {
+
+  @Override
+  public Set<ResourceID> toPrimaryResourceIDs(ConfigCustomResource config) {
+    var targetNames = config.getSpec().getTargetNames();
+    if (targetNames == null || targetNames.isEmpty()) {
+      return Set.of();
+    }
+    var namespace = config.getMetadata().getNamespace();
+    return targetNames.stream()
+        .filter(name -> name != null && !name.isBlank())
+        .map(name -> new ResourceID(name, namespace))
+        .collect(Collectors.toSet());
+  }
+}
diff --git a/operator-framework/src/test/java/io/javaoperatorsdk/operator/baseapi/secondarytoprimaryreferencechange/SecondaryToPrimaryReferenceChangeIT.java b/operator-framework/src/test/java/io/javaoperatorsdk/operator/baseapi/secondarytoprimaryreferencechange/SecondaryToPrimaryReferenceChangeIT.java
new file mode 100644
index 0000000000..37ade3a174
--- /dev/null
+++ b/operator-framework/src/test/java/io/javaoperatorsdk/operator/baseapi/secondarytoprimaryreferencechange/SecondaryToPrimaryReferenceChangeIT.java
@@ -0,0 +1,109 @@
+/*
+ * Copyright Java Operator SDK Authors
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *         http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package io.javaoperatorsdk.operator.baseapi.secondarytoprimaryreferencechange;
+
+import java.time.Duration;
+import java.util.List;
+
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.RegisterExtension;
+
+import io.fabric8.kubernetes.api.model.ObjectMetaBuilder;
+import io.javaoperatorsdk.annotation.Sample;
+import io.javaoperatorsdk.operator.junit.LocallyRunOperatorExtension;
+
+import static io.javaoperatorsdk.operator.baseapi.secondarytoprimaryreferencechange.TargetReconciler.DEFAULT_VALUE;
+import static org.assertj.core.api.Assertions.assertThat;
+import static org.awaitility.Awaitility.await;
+
+@Sample(
+    tldr = "Handling a Secondary Resource Whose References to Primaries Change",
+    description =
+        """
+        Demonstrates a configuration custom resource (the secondary) that references multiple \
+        target custom resources (the primaries) via a spec field and serves as their input. Each \
+        target is reconciled so that, if a config references it, it takes the value from that \
+        config; otherwise it falls back to a default. The test shows how to handle a change of the \
+        referenced set where only a subset changes: a target that is dropped from the references \
+        reverts to the default, a target that stays keeps the value, and a newly referenced target \
+        picks it up.
+        """)
+class SecondaryToPrimaryReferenceChangeIT {
+
+  static final String TARGET_A = "target-a";
+  static final String TARGET_B = "target-b";
+  static final String TARGET_C = "target-c";
+  static final String CONFIG_NAME = "config";
+  static final String CONFIG_VALUE = "value-from-config";
+
+  @RegisterExtension
+  LocallyRunOperatorExtension operator =
+      LocallyRunOperatorExtension.builder()
+          .withAdditionalCustomResourceDefinition(ConfigCustomResource.class)
+          .withReconciler(new TargetReconciler())
+          .build();
+
+  @Test
+  void targetsTakeValueFromReferencingConfigAndHandleSubsetReferenceChange() {
+    operator.create(target(TARGET_A));
+    operator.create(target(TARGET_B));
+    operator.create(target(TARGET_C));
+
+    // With no config, all targets fall back to the default value.
+    awaitTargetValue(TARGET_A, DEFAULT_VALUE);
+    awaitTargetValue(TARGET_B, DEFAULT_VALUE);
+    awaitTargetValue(TARGET_C, DEFAULT_VALUE);
+
+    // A config referencing targets A and B makes both take the config's value; C stays default.
+    var config = operator.create(config(TARGET_A, TARGET_B));
+    awaitTargetValue(TARGET_A, CONFIG_VALUE);
+    awaitTargetValue(TARGET_B, CONFIG_VALUE);
+    awaitTargetValue(TARGET_C, DEFAULT_VALUE);
+
+    // Change a subset of the references: drop A, keep B, add C. A reverts to the default, B keeps
+    // the value, and C now picks it up.
+    config.getSpec().setTargetNames(List.of(TARGET_B, TARGET_C));
+    operator.replace(config);
+
+    awaitTargetValue(TARGET_C, CONFIG_VALUE);
+    awaitTargetValue(TARGET_A, DEFAULT_VALUE);
+    awaitTargetValue(TARGET_B, CONFIG_VALUE);
+  }
+
+  private void awaitTargetValue(String name, String expectedValue) {
+    await()
+        .atMost(Duration.ofSeconds(10))
+        .untilAsserted(
+            () -> {
+              var target = operator.get(TargetCustomResource.class, name);
+              assertThat(target.getStatus()).isNotNull();
+              assertThat(target.getStatus().getValue()).isEqualTo(expectedValue);
+            });
+  }
+
+  private TargetCustomResource target(String name) {
+    var target = new TargetCustomResource();
+    target.setMetadata(new ObjectMetaBuilder().withName(name).build());
+    return target;
+  }
+
+  private ConfigCustomResource config(String... targetNames) {
+    var config = new ConfigCustomResource();
+    config.setMetadata(new ObjectMetaBuilder().withName(CONFIG_NAME).build());
+    config.setSpec(new ConfigSpec().setTargetNames(List.of(targetNames)).setValue(CONFIG_VALUE));
+    return config;
+  }
+}
diff --git a/operator-framework/src/test/java/io/javaoperatorsdk/operator/baseapi/secondarytoprimaryreferencechange/TargetCustomResource.java b/operator-framework/src/test/java/io/javaoperatorsdk/operator/baseapi/secondarytoprimaryreferencechange/TargetCustomResource.java
new file mode 100644
index 0000000000..b3bcae6ccb
--- /dev/null
+++ b/operator-framework/src/test/java/io/javaoperatorsdk/operator/baseapi/secondarytoprimaryreferencechange/TargetCustomResource.java
@@ -0,0 +1,35 @@
+/*
+ * Copyright Java Operator SDK Authors
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *         http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package io.javaoperatorsdk.operator.baseapi.secondarytoprimaryreferencechange;
+
+import io.fabric8.kubernetes.api.model.Namespaced;
+import io.fabric8.kubernetes.client.CustomResource;
+import io.fabric8.kubernetes.model.annotation.Group;
+import io.fabric8.kubernetes.model.annotation.Kind;
+import io.fabric8.kubernetes.model.annotation.ShortNames;
+import io.fabric8.kubernetes.model.annotation.Version;
+
+/**
+ * Primary resource that is reconciled. Its desired status value is provided by a {@link
+ * ConfigCustomResource} that references it (see {@link TargetReconciler}); when no config
+ * references it, a default value is used.
+ */
+@Group("sample.javaoperatorsdk")
+@Version("v1")
+@Kind("SecondaryToPrimaryRefTarget")
+@ShortNames("s2ptarget")
+public class TargetCustomResource extends CustomResource<Void, TargetStatus>
+    implements Namespaced {}
diff --git a/operator-framework/src/test/java/io/javaoperatorsdk/operator/baseapi/secondarytoprimaryreferencechange/TargetReconciler.java b/operator-framework/src/test/java/io/javaoperatorsdk/operator/baseapi/secondarytoprimaryreferencechange/TargetReconciler.java
new file mode 100644
index 0000000000..ee8d11e9d4
--- /dev/null
+++ b/operator-framework/src/test/java/io/javaoperatorsdk/operator/baseapi/secondarytoprimaryreferencechange/TargetReconciler.java
@@ -0,0 +1,78 @@
+/*
+ * Copyright Java Operator SDK Authors
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *         http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package io.javaoperatorsdk.operator.baseapi.secondarytoprimaryreferencechange;
+
+import java.util.List;
+
+import io.javaoperatorsdk.annotation.Sample;
+import io.javaoperatorsdk.operator.api.config.informer.InformerEventSourceConfiguration;
+import io.javaoperatorsdk.operator.api.reconciler.Context;
+import io.javaoperatorsdk.operator.api.reconciler.ControllerConfiguration;
+import io.javaoperatorsdk.operator.api.reconciler.EventSourceContext;
+import io.javaoperatorsdk.operator.api.reconciler.Reconciler;
+import io.javaoperatorsdk.operator.api.reconciler.UpdateControl;
+import io.javaoperatorsdk.operator.processing.event.source.EventSource;
+import io.javaoperatorsdk.operator.processing.event.source.informer.InformerEventSource;
+
+@Sample(
+    tldr = "Reconciling Primaries Driven by a Referencing Secondary Custom Resource",
+    description =
+        """
+        A configuration custom resource (the secondary) references one or more target custom \
+        resources (the primaries) through a spec field and acts as their input. This reconciler \
+        watches those config resources with an InformerEventSource and, on each reconciliation, \
+        sets the target's value from the config that currently references it, falling back to a \
+        default when none does. When a config's set of references changes — including when only a \
+        subset of the referenced targets is replaced — the framework's primary-to-secondary index \
+        reconciles both the newly referenced targets and the ones that are no longer referenced, so \
+        a dropped target reverts to its default.
+        """)
+@ControllerConfiguration
+public class TargetReconciler implements Reconciler<TargetCustomResource> {
+
+  public static final String DEFAULT_VALUE = "default";
+
+  @Override
+  public List<EventSource<?, TargetCustomResource>> prepareEventSources(
+      EventSourceContext<TargetCustomResource> context) {
+
+    var configuration =
+        InformerEventSourceConfiguration.from(
+                ConfigCustomResource.class, TargetCustomResource.class)
+            .withSecondaryToPrimaryMapper(new ConfigToTargetMapper())
+            .build();
+
+    var ies = new InformerEventSource<>(configuration, context);
+    return List.of(ies);
+  }
+
+  @Override
+  public UpdateControl<TargetCustomResource> reconcile(
+      TargetCustomResource target, Context<TargetCustomResource> context) {
+
+    // The framework keeps the primary-to-secondary index up to date on reference changes, so a
+    // config is only associated with the target it currently references. We take the value from
+    // the referencing config, or fall back to the default when none references this target.
+    var value =
+        context
+            .getSecondaryResource(ConfigCustomResource.class)
+            .map(config -> config.getSpec().getValue())
+            .orElse(DEFAULT_VALUE);
+
+    target.setStatus(new TargetStatus().setValue(value));
+    return UpdateControl.patchStatus(target);
+  }
+}
diff --git a/operator-framework/src/test/java/io/javaoperatorsdk/operator/baseapi/secondarytoprimaryreferencechange/TargetStatus.java b/operator-framework/src/test/java/io/javaoperatorsdk/operator/baseapi/secondarytoprimaryreferencechange/TargetStatus.java
new file mode 100644
index 0000000000..3679813070
--- /dev/null
+++ b/operator-framework/src/test/java/io/javaoperatorsdk/operator/baseapi/secondarytoprimaryreferencechange/TargetStatus.java
@@ -0,0 +1,30 @@
+/*
+ * Copyright Java Operator SDK Authors
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *         http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package io.javaoperatorsdk.operator.baseapi.secondarytoprimaryreferencechange;
+
+public class TargetStatus {
+
+  private String value;
+
+  public String getValue() {
+    return value;
+  }
+
+  public TargetStatus setValue(String value) {
+    this.value = value;
+    return this;
+  }
+}