diff --git a/src/gateway/server-startup-plugins.test.ts b/src/gateway/server-startup-plugins.test.ts
index fcc569bff3e..cc65e867ee4 100644
--- a/src/gateway/server-startup-plugins.test.ts
+++ b/src/gateway/server-startup-plugins.test.ts
@@ -308,6 +308,7 @@ describe("prepareGatewayPluginBootstrap runtime-deps staging", () => {
     expect(applyPluginAutoEnable).toHaveBeenCalledWith({
       config: sourceConfig,
       env: process.env,
+      manifestRegistry: pluginManifestRegistry,
     });
     expect(loadPluginLookUpTable).toHaveBeenCalledWith(
       expect.objectContaining({
diff --git a/src/gateway/server-startup-plugins.ts b/src/gateway/server-startup-plugins.ts
index ea1a1f7111c..64d62f02ea8 100644
--- a/src/gateway/server-startup-plugins.ts
+++ b/src/gateway/server-startup-plugins.ts
@@ -140,6 +140,9 @@ export async function prepareGatewayPluginBootstrap(params: {
         activationConfig: applyPluginAutoEnable({
           config: activationSourceConfig,
           env: process.env,
+          ...(params.pluginMetadataSnapshot?.manifestRegistry
+            ? { manifestRegistry: params.pluginMetadataSnapshot.manifestRegistry }
+            : {}),
         }).config,
       });
   const defaultAgentId = resolveDefaultAgentId(gatewayPluginConfig);