diff --git a/x-pack/plugins/ingest_manager/server/services/agent_config.ts b/x-pack/plugins/ingest_manager/server/services/agent_config.ts
index c0eb614102b29a..e5b20de3bf911a 100644
--- a/x-pack/plugins/ingest_manager/server/services/agent_config.ts
+++ b/x-pack/plugins/ingest_manager/server/services/agent_config.ts
@@ -3,6 +3,7 @@
  * or more contributor license agreements. Licensed under the Elastic License;
  * you may not use this file except in compliance with the Elastic License.
  */
+import { uniq } from 'lodash';
 import { SavedObjectsClientContract } from 'kibana/server';
 import { AuthenticatedUser } from '../../../security/server';
 import { DEFAULT_AGENT_CONFIG, AGENT_CONFIG_SAVED_OBJECT_TYPE } from '../constants';
@@ -54,7 +55,7 @@ class AgentConfigService {
     await soClient.update<AgentConfig>(SAVED_OBJECT_TYPE, id, {
       ...agentConfig,
       revision: oldAgentConfig.revision + 1,
-      updated_on: new Date().toString(),
+      updated_on: new Date().toISOString(),
       updated_by: user ? user.username : 'system',
     });
 
@@ -205,7 +206,9 @@ class AgentConfigService {
       id,
       {
         ...oldAgentConfig,
-        datasources: [...((oldAgentConfig.datasources || []) as string[])].concat(datasourceIds),
+        datasources: uniq(
+          [...((oldAgentConfig.datasources || []) as string[])].concat(datasourceIds)
+        ),
       },
       options?.user
     );
@@ -228,8 +231,10 @@ class AgentConfigService {
       id,
       {
         ...oldAgentConfig,
-        datasources: [...((oldAgentConfig.datasources || []) as string[])].filter(
-          dsId => !datasourceIds.includes(dsId)
+        datasources: uniq(
+          [...((oldAgentConfig.datasources || []) as string[])].filter(
+            dsId => !datasourceIds.includes(dsId)
+          )
         ),
       },
       options?.user
diff --git a/x-pack/plugins/ingest_manager/server/services/setup.ts b/x-pack/plugins/ingest_manager/server/services/setup.ts
index f770e9d17ffb15..4b79cd639b6138 100644
--- a/x-pack/plugins/ingest_manager/server/services/setup.ts
+++ b/x-pack/plugins/ingest_manager/server/services/setup.ts
@@ -70,7 +70,7 @@ async function addPackageToConfig(
     savedObjectsClient: soClient,
     pkgkey: `${packageToInstall.name}-${packageToInstall.version}`,
   });
-  const datasource = await datasourceService.create(soClient, {
+  await datasourceService.create(soClient, {
     name: `${packageInfo.name}-1`,
     enabled: true,
     package: {
@@ -82,6 +82,4 @@ async function addPackageToConfig(
     config_id: config.id,
     output_id: defaultOutput.id,
   });
-  // Assign it to the given agent config
-  await agentConfigService.assignDatasources(soClient, datasource.config_id, [datasource.id]);
 }