diff --git a/lib/modules/manager/helmfile/__fixtures__/multidoc.yaml b/lib/modules/manager/helmfile/__fixtures__/multidoc.yaml
index f194b9c30410a9..19f65754151bed 100644
--- a/lib/modules/manager/helmfile/__fixtures__/multidoc.yaml
+++ b/lib/modules/manager/helmfile/__fixtures__/multidoc.yaml
@@ -26,6 +26,8 @@ repositories:
 - name: prometheus-community
   url: https://prometheus-community.github.io/helm-charts
 
+---
+
 templates:
   external-chart: &external-chart
     missingFileHandler: Debug
diff --git a/lib/modules/manager/helmfile/extract.spec.ts b/lib/modules/manager/helmfile/extract.spec.ts
index 279c57cd6e051a..abbddc6badf65b 100644
--- a/lib/modules/manager/helmfile/extract.spec.ts
+++ b/lib/modules/manager/helmfile/extract.spec.ts
@@ -1,3 +1,4 @@
+import { codeBlock } from 'common-tags';
 import { Fixtures } from '../../../../test/fixtures';
 import { fs } from '../../../../test/util';
 import { GlobalConfig } from '../../../config/global';
@@ -14,6 +15,19 @@ describe('modules/manager/helmfile/extract', () => {
       GlobalConfig.set({ localDir });
     });
 
+    it('skip null YAML document', async () => {
+      const content = codeBlock`
+        ~
+        `;
+      const fileName = 'helmfile.yaml';
+      const result = await extractPackageFile(content, fileName, {
+        registryAliases: {
+          stable: 'https://charts.helm.sh/stable',
+        },
+      });
+      expect(result).toBeNull();
+    });
+
     it('returns null if no releases', async () => {
       const content = `
       repositories:
diff --git a/lib/modules/manager/helmfile/extract.ts b/lib/modules/manager/helmfile/extract.ts
index 379073c0c08f84..237a15157a09cf 100644
--- a/lib/modules/manager/helmfile/extract.ts
+++ b/lib/modules/manager/helmfile/extract.ts
@@ -31,7 +31,7 @@ export async function extractPackageFile(
 ): Promise<PackageFileContent | null> {
   const deps: PackageDependency[] = [];
   let docs: Doc[];
-  const registryAliases: Record<string, string> = {};
+  let registryAliases: Record<string, string> = {};
   // Record kustomization usage for all deps, since updating artifacts is run on the helmfile.yaml as a whole.
   let needKustomize = false;
   try {
@@ -47,16 +47,26 @@ export async function extractPackageFile(
     return null;
   }
   for (const doc of docs) {
-    if (!(doc && is.array(doc.releases))) {
+    if (!doc) {
       continue;
     }
 
+    // Always check for repositories in the current document and override the existing ones if any (as YAML does)
     if (doc.repositories) {
+      registryAliases = {};
       for (let i = 0; i < doc.repositories.length; i += 1) {
         registryAliases[doc.repositories[i].name] = doc.repositories[i].url;
       }
+      logger.debug(
+        { registryAliases, packageFile },
+        `repositories discovered.`,
+      );
+    }
+
+    // Skip extraction if the document contains no releases
+    if (!is.array(doc.releases)) {
+      continue;
     }
-    logger.debug({ registryAliases }, 'repositories discovered.');
 
     for (const dep of doc.releases) {
       let depName = dep.chart;