diff --git a/x-pack/plugins/fleet/server/services/secrets.test.ts b/x-pack/plugins/fleet/server/services/secrets.test.ts
index 8e92836e3fbf4..729c74a3ddec0 100644
--- a/x-pack/plugins/fleet/server/services/secrets.test.ts
+++ b/x-pack/plugins/fleet/server/services/secrets.test.ts
@@ -1018,9 +1018,11 @@ describe('secrets', () => {
       it('returns single secret reference for required secret', async () => {
         const mockPackagePolicy = {
           vars: {
-            'pkg-secret-1': {
-              value: 'pkg-secret-1-val',
+            'pkg-secret-1': {},
+            'pkg-secret-2': {
+              value: 'pkg-secret-2-val',
             },
+            'dot-notation.stream.pkg-secret-3': {},
           },
           inputs: [],
         } as unknown as NewPackagePolicy;
@@ -1198,6 +1200,7 @@ describe('secrets', () => {
               value: 'pkg-secret-1-val',
             },
             'pkg-secret-2': {},
+            'dot-notation.pkg-secret-3': {},
           },
           inputs: [],
         } as unknown as PackagePolicy;
diff --git a/x-pack/plugins/fleet/server/services/secrets.ts b/x-pack/plugins/fleet/server/services/secrets.ts
index 6f50b2cd8b73b..c01c64e37e59e 100644
--- a/x-pack/plugins/fleet/server/services/secrets.ts
+++ b/x-pack/plugins/fleet/server/services/secrets.ts
@@ -241,7 +241,11 @@ export async function extractAndWriteSecrets(opts: {
     values: secretsToCreate.map((secretPath) => secretPath.value.value),
   });
 
-  const policyWithSecretRefs = getPolicyWithSecretReferences(secretPaths, secrets, packagePolicy);
+  const policyWithSecretRefs = getPolicyWithSecretReferences(
+    secretsToCreate,
+    secrets,
+    packagePolicy
+  );
 
   return {
     packagePolicy: policyWithSecretRefs,