diff --git a/x-pack/plugins/ingest_manager/server/services/agents/acks.ts b/x-pack/plugins/ingest_manager/server/services/agents/acks.ts
index e391e81ebd0a62..c59bac6a5469ac 100644
--- a/x-pack/plugins/ingest_manager/server/services/agents/acks.ts
+++ b/x-pack/plugins/ingest_manager/server/services/agents/acks.ts
@@ -92,8 +92,9 @@ function getLatestConfigIfUpdated(agent: Agent, actions: AgentAction[]) {
 
 function buildUpdateAgentConfig(agentId: string, config: FullAgentConfig) {
   const packages = config.inputs.reduce<string[]>((acc, input) => {
-    if (input.package && input.package.name && acc.indexOf(input.package.name) < 0) {
-      return [input.package.name, ...acc];
+    const packageName = input.meta?.package?.name;
+    if (packageName && acc.indexOf(packageName) < 0) {
+      return [packageName, ...acc];
     }
     return acc;
   }, []);
diff --git a/x-pack/test/api_integration/apis/fleet/agent_flow.ts b/x-pack/test/api_integration/apis/fleet/agent_flow.ts
index e9e9f0e0208e46..08b97ad32ae296 100644
--- a/x-pack/test/api_integration/apis/fleet/agent_flow.ts
+++ b/x-pack/test/api_integration/apis/fleet/agent_flow.ts
@@ -26,7 +26,7 @@ export default function (providerContext: FtrProviderContext) {
     });
 
     it('should work', async () => {
-      // 1. Get enrollment token
+      // Get enrollment token
       const { body: enrollmentApiKeysResponse } = await supertest
         .get(`/api/ingest_manager/fleet/enrollment-api-keys`)
         .expect(200);
@@ -40,7 +40,7 @@ export default function (providerContext: FtrProviderContext) {
 
       expect(enrollmentApiKeyResponse.item).to.have.key('api_key');
       const enrollmentAPIToken = enrollmentApiKeyResponse.item.api_key;
-      // 2. Enroll agent
+      // Enroll agent
       const { body: enrollmentResponse } = await supertestWithoutAuth
         .post(`/api/ingest_manager/fleet/agents/enroll`)
         .set('kbn-xsrf', 'xxx')
@@ -48,7 +48,11 @@ export default function (providerContext: FtrProviderContext) {
         .send({
           type: 'PERMANENT',
           metadata: {
-            local: {},
+            local: {
+              elastic: {
+                agent: { version: 'TODO' },
+              },
+            },
             user_provided: {},
           },
         })
@@ -57,7 +61,7 @@ export default function (providerContext: FtrProviderContext) {
 
       const agentAccessAPIKey = enrollmentResponse.item.access_api_key;
 
-      // 3. agent checkin
+      // Agent checkin
       const { body: checkinApiResponse } = await supertestWithoutAuth
         .post(`/api/ingest_manager/fleet/agents/${enrollmentResponse.item.id}/checkin`)
         .set('kbn-xsrf', 'xx')
@@ -73,7 +77,7 @@ export default function (providerContext: FtrProviderContext) {
       const configChangeAction = checkinApiResponse.actions[0];
       const defaultOutputApiKey = configChangeAction.data.config.outputs.default.api_key;
 
-      // 4. ack actions
+      // Ack actions
       const { body: ackApiResponse } = await supertestWithoutAuth
         .post(`/api/ingest_manager/fleet/agents/${enrollmentResponse.item.id}/acks`)
         .set('Authorization', `ApiKey ${agentAccessAPIKey}`)
@@ -95,7 +99,7 @@ export default function (providerContext: FtrProviderContext) {
         .expect(200);
       expect(ackApiResponse.success).to.eql(true);
 
-      // 4. second agent checkin
+      // Second agent checkin
       const { body: secondCheckinApiResponse } = await supertestWithoutAuth
         .post(`/api/ingest_manager/fleet/agents/${enrollmentResponse.item.id}/checkin`)
         .set('kbn-xsrf', 'xx')
@@ -107,14 +111,25 @@ export default function (providerContext: FtrProviderContext) {
       expect(secondCheckinApiResponse.success).to.eql(true);
       expect(secondCheckinApiResponse.actions).length(0);
 
-      // 5. unenroll agent
+      // Get agent
+      const { body: getAgentApiResponse } = await supertest
+        .get(`/api/ingest_manager/fleet/agents/${enrollmentResponse.item.id}`)
+        .expect(200);
+
+      expect(getAgentApiResponse.success).to.eql(true);
+      expect(getAgentApiResponse.item.packages).to.contain(
+        'system',
+        "Agent should run the 'system' package"
+      );
+
+      // Unenroll agent
       const { body: unenrollResponse } = await supertest
         .post(`/api/ingest_manager/fleet/agents/${enrollmentResponse.item.id}/unenroll`)
         .set('kbn-xsrf', 'xx')
         .expect(200);
       expect(unenrollResponse.success).to.eql(true);
 
-      // 6. Checkin after unenrollment
+      // Checkin after unenrollment
       await supertestWithoutAuth
         .post(`/api/ingest_manager/fleet/agents/${enrollmentResponse.item.id}/checkin`)
         .set('kbn-xsrf', 'xx')