diff --git a/x-pack/plugins/fleet/server/services/epm/elasticsearch/ingest_pipeline/remove.ts b/x-pack/plugins/fleet/server/services/epm/elasticsearch/ingest_pipeline/remove.ts
index f12d68190b4ac..4acc4767de525 100644
--- a/x-pack/plugins/fleet/server/services/epm/elasticsearch/ingest_pipeline/remove.ts
+++ b/x-pack/plugins/fleet/server/services/epm/elasticsearch/ingest_pipeline/remove.ts
@@ -8,6 +8,7 @@
 import { SavedObjectsClientContract } from 'src/core/server';
 import { appContextService } from '../../../';
 import { CallESAsCurrentUser, ElasticsearchAssetType } from '../../../../types';
+import { IngestManagerError } from '../../../../errors';
 import { getInstallation } from '../../packages/get';
 import { PACKAGES_SAVED_OBJECT_TYPE, EsAssetReference } from '../../../../../common';
 
@@ -61,7 +62,11 @@ export async function deletePipeline(callCluster: CallESAsCurrentUser, id: strin
     try {
       await callCluster('ingest.deletePipeline', { id });
     } catch (err) {
-      throw new Error(`error deleting pipeline ${id}`);
+      // Only throw if error is not a 404 error. Sometimes the pipeline is already deleted, but we have
+      // duplicate references to them, see https://github.com/elastic/kibana/issues/91192
+      if (err.statusCode !== 404) {
+        throw new IngestManagerError(`error deleting pipeline ${id}: ${err}`);
+      }
     }
   }
 }
diff --git a/x-pack/plugins/fleet/server/services/epm/elasticsearch/transform/install.ts b/x-pack/plugins/fleet/server/services/epm/elasticsearch/transform/install.ts
index 57e1090f8954b..948a9c56746f3 100644
--- a/x-pack/plugins/fleet/server/services/epm/elasticsearch/transform/install.ts
+++ b/x-pack/plugins/fleet/server/services/epm/elasticsearch/transform/install.ts
@@ -42,9 +42,13 @@ export const installTransform = async (
     previousInstalledTransformEsAssets = installation.installed_es.filter(
       ({ type, id }) => type === ElasticsearchAssetType.transform
     );
-    logger.info(
-      `Found previous transform references:\n ${JSON.stringify(previousInstalledTransformEsAssets)}`
-    );
+    if (previousInstalledTransformEsAssets.length) {
+      logger.info(
+        `Found previous transform references:\n ${JSON.stringify(
+          previousInstalledTransformEsAssets
+        )}`
+      );
+    }
   }
 
   // delete all previous transform
diff --git a/x-pack/plugins/fleet/server/services/epm/elasticsearch/transform/remove.ts b/x-pack/plugins/fleet/server/services/epm/elasticsearch/transform/remove.ts
index b08b7cb7f1ec8..0e947e0f0b90b 100644
--- a/x-pack/plugins/fleet/server/services/epm/elasticsearch/transform/remove.ts
+++ b/x-pack/plugins/fleet/server/services/epm/elasticsearch/transform/remove.ts
@@ -26,7 +26,9 @@ export const deleteTransforms = async (
   transformIds: string[]
 ) => {
   const logger = appContextService.getLogger();
-  logger.info(`Deleting currently installed transform ids ${transformIds}`);
+  if (transformIds.length) {
+    logger.info(`Deleting currently installed transform ids ${transformIds}`);
+  }
   await Promise.all(
     transformIds.map(async (transformId) => {
       // get the index the transform