diff --git a/packages/storage/src/__tests__/operational-state-store.test.ts b/packages/storage/src/__tests__/operational-state-store.test.ts
index 4c46073f295..9162405f83d 100644
--- a/packages/storage/src/__tests__/operational-state-store.test.ts
+++ b/packages/storage/src/__tests__/operational-state-store.test.ts
@@ -89,6 +89,23 @@ test('new runtime databases use incremental vacuum before operational schema cre
   }
 });
 
+test('an operational opener configures the empty file left by another connection', async () => {
+  const root = await mkdtemp(join(tmpdir(), 'maka-operational-empty-open-'));
+  const first = new DatabaseSync(join(root, 'runtime.sqlite'));
+  try {
+    const lease = acquireOperationalStateDatabase(root);
+    try {
+      assert.equal(lease.database.prepare('PRAGMA auto_vacuum').get()?.auto_vacuum, 2);
+      assert.equal(first.prepare('PRAGMA auto_vacuum').get()?.auto_vacuum, 2);
+    } finally {
+      lease.close();
+    }
+  } finally {
+    first.close();
+    await rm(root, { recursive: true, force: true });
+  }
+});
+
 test('workflow 12 upgrade adds wait storage atomically and preserves every released row and schema scope', async () => {
   const root = await mkdtemp(join(tmpdir(), 'maka-operational-workflow-12-'));
   const databasePath = join(root, 'runtime.sqlite');
diff --git a/packages/storage/src/__tests__/sqlite-recovery-concurrency.test.ts b/packages/storage/src/__tests__/sqlite-recovery-concurrency.test.ts
index 35de68bff55..3af4c65b69c 100644
--- a/packages/storage/src/__tests__/sqlite-recovery-concurrency.test.ts
+++ b/packages/storage/src/__tests__/sqlite-recovery-concurrency.test.ts
@@ -236,6 +236,7 @@ describe('SQLite recovery authority multi-process races', () => {
               .user_version,
             SQLITE_RUNTIME_SCHEMA_VERSION,
           );
+          assert.equal(database.prepare('PRAGMA auto_vacuum').get()?.auto_vacuum, 2);
         } finally {
           database.close();
         }
diff --git a/packages/storage/src/__tests__/sqlite-runtime-store.test.ts b/packages/storage/src/__tests__/sqlite-runtime-store.test.ts
index e4b8452973e..8bdfdef42ce 100644
--- a/packages/storage/src/__tests__/sqlite-runtime-store.test.ts
+++ b/packages/storage/src/__tests__/sqlite-runtime-store.test.ts
@@ -127,6 +127,35 @@ describe('SqliteRuntimeStore', () => {
     });
   });
 
+  it('configures incremental auto-vacuum when another opener created the empty file', async () => {
+    const root = await mkdtemp(join(tmpdir(), 'maka-sqlite-runtime-empty-open-'));
+    const dbPath = join(root, 'runtime.sqlite');
+    const first = new DatabaseSync(dbPath);
+    try {
+      const store = createSqliteRuntimeStore(dbPath);
+      store.close();
+      assert.equal(first.prepare('PRAGMA auto_vacuum').get()?.auto_vacuum, 2);
+    } finally {
+      first.close();
+      await rm(root, { recursive: true, force: true });
+    }
+  });
+
+  it('preserves an initialized NONE database even when it has no tables', async () => {
+    const root = await mkdtemp(join(tmpdir(), 'maka-sqlite-runtime-empty-none-'));
+    const dbPath = join(root, 'runtime.sqlite');
+    const first = new DatabaseSync(dbPath);
+    try {
+      first.exec('BEGIN IMMEDIATE; COMMIT');
+      const store = createSqliteRuntimeStore(dbPath);
+      store.close();
+      assert.equal(first.prepare('PRAGMA auto_vacuum').get()?.auto_vacuum, 0);
+    } finally {
+      first.close();
+      await rm(root, { recursive: true, force: true });
+    }
+  });
+
   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 a111215528d..ba657bd5b5b 100644
--- a/packages/storage/src/operational-state-store.ts
+++ b/packages/storage/src/operational-state-store.ts
@@ -226,7 +226,7 @@ class OperationalStateDatabaseOwner {
       configureSqliteRuntimeLockWait(this.database);
       this.database.exec('PRAGMA foreign_keys = ON');
       if (options.schemaMigration !== 'require_current') {
-        configureSqliteRuntimeAutoVacuumForNewDatabase(this.database, databaseExisted);
+        configureSqliteRuntimeAutoVacuumForNewDatabase(this.database);
       }
       if (options.schemaMigration === 'require_current') {
         requireCurrentOperationalState(this.database);
diff --git a/packages/storage/src/sqlite-runtime-schema.ts b/packages/storage/src/sqlite-runtime-schema.ts
index 5591162eec6..e2ae018706e 100644
--- a/packages/storage/src/sqlite-runtime-schema.ts
+++ b/packages/storage/src/sqlite-runtime-schema.ts
@@ -954,16 +954,13 @@ 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;
+/** Set the reclamation mode before an uninitialized database gets its first page. */
+export function configureSqliteRuntimeAutoVacuumForNewDatabase(db: DatabaseSync): void {
+  // Another opener may have created the file without initializing its header.
+  // File existence cannot tell us whether it still needs this configuration.
+  // Preserve initialized databases, including those with no application tables.
+  const pages = db.prepare('PRAGMA page_count').get() as { page_count: number };
+  if (pages.page_count !== 0) return;
   db.exec('PRAGMA auto_vacuum = INCREMENTAL');
   const configured = db.prepare('PRAGMA auto_vacuum').get() as
     | { auto_vacuum?: unknown }
diff --git a/packages/storage/src/sqlite-runtime-store.ts b/packages/storage/src/sqlite-runtime-store.ts
index ceb3cf9b188..96df894ea83 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 { existsSync, mkdirSync } from 'node:fs';
+import { mkdirSync } from 'node:fs';
 import { createRequire } from 'node:module';
 import { dirname } from 'node:path';
 import type { DatabaseSync, SQLInputValue } from 'node:sqlite';
@@ -134,6 +134,7 @@ import {
 import {
   configureSqliteRuntimeDatabase,
   configureSqliteRuntimeAutoVacuumForNewDatabase,
+  configureSqliteRuntimeLockWait,
   migrateSqliteRuntimeDatabase,
   readUserVersion,
   RUNTIME_RECOVERY_AUTHORITY_CAPABILITY,
@@ -346,7 +347,6 @@ 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);
@@ -360,7 +360,8 @@ export class SqliteRuntimeStore
           );
         }
       } else {
-        configureSqliteRuntimeAutoVacuumForNewDatabase(this.db, databaseExisted);
+        configureSqliteRuntimeLockWait(this.db);
+        configureSqliteRuntimeAutoVacuumForNewDatabase(this.db);
         configureSqliteRuntimeDatabase(this.db);
         migrateSqliteRuntimeDatabase(this.db);
       }