diff --git a/packages/backend-defaults/src/entrypoints/database/DatabaseManager.test.ts b/packages/backend-defaults/src/entrypoints/database/DatabaseManager.test.ts
index 630dfa6061..0d52ff16ff 100644
--- a/packages/backend-defaults/src/entrypoints/database/DatabaseManager.test.ts
+++ b/packages/backend-defaults/src/entrypoints/database/DatabaseManager.test.ts
@@ -96,17 +96,47 @@ describe('DatabaseManagerImpl', () => {
     expect(connector2.getClient).toHaveBeenLastCalledWith('plugin2', undefined);
   });
 
-  it('retains the migration skip info', async () => {
+  it('migration skip options take precedence over config', async () => {
     const connector = {
       getClient: jest.fn(),
       dropDatabase: jest.fn(),
     } satisfies Connector;
 
+    const impl = new DatabaseManagerImpl(
+      new ConfigReader({
+        client: 'pg',
+        backend: {
+          database: {
+            skipMigrations: true,
+            plugin: { plugin1: { skipMigrations: true } },
+          },
+        },
+      }),
+      {
+        pg: connector,
+      },
+      { migrations: { skip: false } },
+    );
+    expect((await impl.forPlugin('plugin1')).migrations).toEqual({
+      skip: false,
+    });
+
     const impl1 = new DatabaseManagerImpl(new ConfigReader({ client: 'pg' }), {
       pg: connector,
     });
 
-    const impl2 = new DatabaseManagerImpl(
+    expect((await impl1.forPlugin('plugin1')).migrations).toEqual({
+      skip: false,
+    });
+  });
+
+  it('plugin can skip migrations using config', async () => {
+    const connector = {
+      getClient: jest.fn(),
+      dropDatabase: jest.fn(),
+    } satisfies Connector;
+
+    const impl = new DatabaseManagerImpl(
       new ConfigReader({
         client: 'pg',
         backend: {
@@ -118,15 +148,14 @@ describe('DatabaseManagerImpl', () => {
       },
     );
 
-    expect((await impl1.forPlugin('plugin1')).migrations).toEqual({
+    expect((await impl.forPlugin('plugin1')).migrations).toEqual({
+      skip: true,
+    });
+    expect((await impl.forPlugin('plugin2')).migrations).toEqual({
       skip: false,
     });
 
-    expect((await impl2.forPlugin('plugin1')).migrations).toEqual({
-      skip: true,
-    });
-
-    const impl3 = new DatabaseManagerImpl(
+    const impl2 = new DatabaseManagerImpl(
       new ConfigReader({
         client: 'pg',
         backend: {
@@ -140,7 +169,10 @@ describe('DatabaseManagerImpl', () => {
         pg: connector,
       },
     );
-    expect((await impl3.forPlugin('plugin1')).migrations).toEqual({
+    expect((await impl2.forPlugin('plugin1')).migrations).toEqual({
+      skip: false,
+    });
+    expect((await impl2.forPlugin('plugin2')).migrations).toEqual({
       skip: true,
     });
   });
diff --git a/packages/backend-defaults/src/entrypoints/database/DatabaseManager.ts b/packages/backend-defaults/src/entrypoints/database/DatabaseManager.ts
index f756e11aac..5c39307f27 100644
--- a/packages/backend-defaults/src/entrypoints/database/DatabaseManager.ts
+++ b/packages/backend-defaults/src/entrypoints/database/DatabaseManager.ts
@@ -41,6 +41,7 @@ function pluginPath(pluginId: string): string {
  * @public
  */
 export type DatabaseManagerOptions = {
+  migrations?: DatabaseService['migrations'];
   logger?: LoggerService;
 };
 
@@ -86,16 +87,20 @@ export class DatabaseManagerImpl implements LegacyRootDatabaseService {
     }
     const getClient = () => this.getDatabase(pluginId, connector, deps);
 
-    const migrationConfig =
-      this.config.getOptionalBoolean('backend.database.skipMigrations') ||
-      this.config.getOptionalBoolean(
-        `backend.database.plugin.${pluginId}.skipMigrations`,
-      );
-    const migrations = {
-      skip: migrationConfig || false,
-    };
+    let skip = false;
+    // config options take precedence over config
+    if (this.options?.migrations?.skip !== undefined) {
+      skip = this.options.migrations.skip;
+    } else {
+      skip =
+        this.config.getOptionalBoolean(
+          `backend.database.plugin.${pluginId}.skipMigrations`,
+        ) ??
+        this.config.getOptionalBoolean('backend.database.skipMigrations') ??
+        false;
+    }
 
-    return { getClient, migrations };
+    return { getClient, migrations: { skip } };
   }
 
   /**