diff --git a/x-pack/plugins/fleet/server/services/epm/elasticsearch/ingest_pipeline/install.test.ts b/x-pack/plugins/fleet/server/services/epm/elasticsearch/ingest_pipeline/install.test.ts
index d69fd167ee117..7ea61bde7a0e8 100644
--- a/x-pack/plugins/fleet/server/services/epm/elasticsearch/ingest_pipeline/install.test.ts
+++ b/x-pack/plugins/fleet/server/services/epm/elasticsearch/ingest_pipeline/install.test.ts
@@ -39,6 +39,14 @@ describe('Install pipeline tests', () => {
       await res.install(esClient, logger);
 
       expect(esClient.ingest.putPipeline).toBeCalled();
+
+      // It should add the @custom pipeline for the main pipeline
+      const pipelinesWithCustomProcessor = esClient.ingest.putPipeline.mock.calls.filter((call) =>
+        // @ts-ignore-error
+        call[0]?.body.includes('@custom')
+      );
+
+      expect(pipelinesWithCustomProcessor).toHaveLength(1);
     });
 
     it('should work with datastream with ingest pipelines define in the package', async () => {
@@ -73,6 +81,14 @@ describe('Install pipeline tests', () => {
       await res.install(esClient, logger);
 
       expect(esClient.ingest.putPipeline).toBeCalledTimes(2);
+
+      // It should add the @custom pipeline only for the main pipeline
+      const pipelinesWithCustomProcessor = esClient.ingest.putPipeline.mock.calls.filter((call) =>
+        // @ts-ignore-error
+        call[0]?.body.includes('@custom')
+      );
+
+      expect(pipelinesWithCustomProcessor).toHaveLength(1);
     });
   });
 });
diff --git a/x-pack/plugins/fleet/server/services/epm/elasticsearch/ingest_pipeline/install.ts b/x-pack/plugins/fleet/server/services/epm/elasticsearch/ingest_pipeline/install.ts
index 2d9fdb31036e7..7ada81c26c926 100644
--- a/x-pack/plugins/fleet/server/services/epm/elasticsearch/ingest_pipeline/install.ts
+++ b/x-pack/plugins/fleet/server/services/epm/elasticsearch/ingest_pipeline/install.ts
@@ -157,7 +157,8 @@ export async function installAllPipelines({
   let datastreamPipelineCreated = false;
   pipelinePaths.forEach((path) => {
     const { name, extension } = getNameAndExtension(path);
-    if (name === dataStream?.ingest_pipeline) {
+    const isMainPipeline = name === dataStream?.ingest_pipeline;
+    if (isMainPipeline) {
       datastreamPipelineCreated = true;
     }
     const nameForInstallation = getPipelineNameForInstallation({
@@ -168,9 +169,8 @@ export async function installAllPipelines({
     const content = getAsset(path).toString('utf-8');
     pipelinesInfos.push({
       nameForInstallation,
-      customIngestPipelineNameForInstallation: dataStream
-        ? getCustomPipelineNameForDatastream(dataStream)
-        : undefined,
+      customIngestPipelineNameForInstallation:
+        dataStream && isMainPipeline ? getCustomPipelineNameForDatastream(dataStream) : undefined,
       content,
       extension,
     });