diff --git a/packages/storage/src/__tests__/operational-state-store.test.ts b/packages/storage/src/__tests__/operational-state-store.test.ts
index f2b5129fbd..651120ec43 100644
--- a/packages/storage/src/__tests__/operational-state-store.test.ts
+++ b/packages/storage/src/__tests__/operational-state-store.test.ts
@@ -69,6 +69,23 @@ test('shares one operational database and produces an online backup', async () =
   }
 });
 
+test('new runtime databases use incremental vacuum before operational schema creation', async () => {
+  const root = await mkdtemp(join(tmpdir(), 'maka-operational-incremental-vacuum-'));
+  try {
+    const lease = acquireOperationalStateDatabase(root);
+    try {
+      assert.equal(
+        (lease.database.prepare('PRAGMA auto_vacuum').get() as { auto_vacuum: number }).auto_vacuum,
+        2,
+      );
+    } finally {
+      lease.close();
+    }
+  } finally {
+    await rm(root, { recursive: true, force: true });
+  }
+});
+
 test('atomically reapplies current owner schema without republishing its registry', async () => {
   const root = await mkdtemp(join(tmpdir(), 'maka-operational-current-convergence-'));
   const databasePath = join(root, 'runtime.sqlite');
diff --git a/packages/storage/src/__tests__/sqlite-runtime-store.test.ts b/packages/storage/src/__tests__/sqlite-runtime-store.test.ts
index ab9aa0f4f4..d490e77b3c 100644
--- a/packages/storage/src/__tests__/sqlite-runtime-store.test.ts
+++ b/packages/storage/src/__tests__/sqlite-runtime-store.test.ts
@@ -64,6 +64,48 @@ const PREFIX_PROOF_TEST_BUDGET = {
 };
 
 describe('SqliteRuntimeStore', () => {
+  it('leaves an existing NONE auto-vacuum database unchanged', async () => {
+    const root = await mkdtemp(join(tmpdir(), 'maka-sqlite-runtime-existing-none-'));
+    const dbPath = join(root, 'runtime.sqlite');
+    const existing = new DatabaseSync(dbPath);
+    existing.exec('CREATE TABLE existing_data (value TEXT NOT NULL)');
+    existing.close();
+    try {
+      const store = createSqliteRuntimeStore(dbPath);
+      store.close();
+      const inspected = new DatabaseSync(dbPath, { readOnly: true });
+      try {
+        assert.equal(
+          (inspected.prepare('PRAGMA auto_vacuum').get() as { auto_vacuum: number }).auto_vacuum,
+          0,
+        );
+        assert.ok(
+          inspected
+            .prepare("SELECT 1 FROM sqlite_schema WHERE type = 'table' AND name = 'existing_data'")
+            .get(),
+        );
+      } finally {
+        inspected.close();
+      }
+    } finally {
+      await rm(root, { recursive: true, force: true });
+    }
+  });
+
+  it('creates runtime databases with incremental auto-vacuum', async () => {
+    await withStore(async (_store, dbPath) => {
+      const inspected = new DatabaseSync(dbPath, { readOnly: true });
+      try {
+        assert.equal(
+          (inspected.prepare('PRAGMA auto_vacuum').get() as { auto_vacuum: number }).auto_vacuum,
+          2,
+        );
+      } finally {
+        inspected.close();
+      }
+    });
+  });
+
   it('reads a complete Session from one snapshot while another connection commits its terminal', async (t) => {
     await withStore(async (store, dbPath) => {
       const opening = invocationOpeningEvent(1);
diff --git a/packages/storage/src/operational-state-store.ts b/packages/storage/src/operational-state-store.ts
index eb80fe0280..a111215528 100644
--- a/packages/storage/src/operational-state-store.ts
+++ b/packages/storage/src/operational-state-store.ts
@@ -23,6 +23,7 @@ import { createRequire } from 'node:module';
 import type { DatabaseSync } from 'node:sqlite';
 import {
   configureSqliteRuntimeDatabase,
+  configureSqliteRuntimeAutoVacuumForNewDatabase,
   configureSqliteRuntimeLockWait,
   migrateSqliteRuntimeDatabase,
   readUserVersion,
@@ -208,7 +209,8 @@ class OperationalStateDatabaseOwner {
     readonly databasePath: string,
     options: OperationalStateDatabaseOptions,
   ) {
-    if (options.schemaMigration === 'require_current' && !existsSync(databasePath)) {
+    const databaseExisted = existsSync(databasePath);
+    if (options.schemaMigration === 'require_current' && !databaseExisted) {
       throw new OperationalStateMigrationBlockedError(
         new Error('Operational state has not been initialized by its Runtime Host'),
         'requires_host_migration',
@@ -223,6 +225,9 @@ class OperationalStateDatabaseOwner {
     try {
       configureSqliteRuntimeLockWait(this.database);
       this.database.exec('PRAGMA foreign_keys = ON');
+      if (options.schemaMigration !== 'require_current') {
+        configureSqliteRuntimeAutoVacuumForNewDatabase(this.database, databaseExisted);
+      }
       if (options.schemaMigration === 'require_current') {
         requireCurrentOperationalState(this.database);
       } else {
diff --git a/packages/storage/src/sqlite-runtime-schema.ts b/packages/storage/src/sqlite-runtime-schema.ts
index e1e8d5b181..5591162eec 100644
--- a/packages/storage/src/sqlite-runtime-schema.ts
+++ b/packages/storage/src/sqlite-runtime-schema.ts
@@ -954,6 +954,25 @@ export function configureSqliteRuntimeDatabase(db: DatabaseSync): void {
   db.exec('PRAGMA foreign_keys = ON');
 }
 
+/** Set the reclamation mode before schema creation on a newly created file only. */
+export function configureSqliteRuntimeAutoVacuumForNewDatabase(
+  db: DatabaseSync,
+  databaseExisted: boolean,
+): void {
+  if (databaseExisted) return;
+  const existingSchema = db
+    .prepare("SELECT 1 AS present FROM sqlite_schema WHERE name NOT LIKE 'sqlite_%' LIMIT 1")
+    .get() as { present?: unknown } | undefined;
+  if (existingSchema?.present === 1) return;
+  db.exec('PRAGMA auto_vacuum = INCREMENTAL');
+  const configured = db.prepare('PRAGMA auto_vacuum').get() as
+    | { auto_vacuum?: unknown }
+    | undefined;
+  if (configured?.auto_vacuum !== 2) {
+    throw new Error('New SQLite runtime database did not enable incremental auto-vacuum');
+  }
+}
+
 /** Configure connection-local lock waiting without changing persistent database state. */
 export function configureSqliteRuntimeLockWait(db: DatabaseSync): void {
   db.exec(`PRAGMA busy_timeout = ${SQLITE_INITIALIZATION_BUSY_TIMEOUT_MS}`);
diff --git a/packages/storage/src/sqlite-runtime-store.ts b/packages/storage/src/sqlite-runtime-store.ts
index 25bcb45421..06b0d973ab 100644
--- a/packages/storage/src/sqlite-runtime-store.ts
+++ b/packages/storage/src/sqlite-runtime-store.ts
@@ -36,7 +36,7 @@ export type {
   ImmutableRuntimePrefixProofReadBudget,
 } from './runtime-event-store-contract.js';
 
-import { mkdirSync } from 'node:fs';
+import { existsSync, mkdirSync } from 'node:fs';
 import { createRequire } from 'node:module';
 import { dirname } from 'node:path';
 import type { DatabaseSync, SQLInputValue } from 'node:sqlite';
@@ -133,6 +133,7 @@ import {
 } from '@maka/core/tool-recovery-bundle';
 import {
   configureSqliteRuntimeDatabase,
+  configureSqliteRuntimeAutoVacuumForNewDatabase,
   migrateSqliteRuntimeDatabase,
   readUserVersion,
   RUNTIME_RECOVERY_AUTHORITY_CAPABILITY,
@@ -345,6 +346,7 @@ export class SqliteRuntimeStore
       return;
     }
     const DatabaseSync = loadDatabaseSync();
+    const databaseExisted = path !== ':memory:' && existsSync(path);
     this.db = options.readOnly
       ? new DatabaseSync(path, { readOnly: true })
       : new DatabaseSync(path);
@@ -358,6 +360,7 @@ export class SqliteRuntimeStore
           );
         }
       } else {
+        configureSqliteRuntimeAutoVacuumForNewDatabase(this.db, databaseExisted);
         configureSqliteRuntimeDatabase(this.db);
         migrateSqliteRuntimeDatabase(this.db);
       }