diff --git a/docs/user-guide/helm.md b/docs/user-guide/helm.md
index 74c67a91e17e9..2a9783a1f0d07 100644
--- a/docs/user-guide/helm.md
+++ b/docs/user-guide/helm.md
@@ -220,8 +220,8 @@ source:
         value: path/to/file.ext
 ```
 
-!!! warning "Reference in multiple sources not supported"
-    Please note that using a multiple sources application will not let you load the file by reference. See [argoproj/argo-cd#13220](https://github.com/argoproj/argo-cd/issues/13220)
+!!! warning "Reference in multiple sources not supported prior to ArgoCD 2.12"
+    Please note that using a multiple sources application will not let you load the file by reference when using ArgoCD versions prior to 2.12
 
 ## Helm Release Name
 
diff --git a/reposerver/repository/repository.go b/reposerver/repository/repository.go
index 83cc149f68c8a..132d122f445fa 100644
--- a/reposerver/repository/repository.go
+++ b/reposerver/repository/repository.go
@@ -474,7 +474,13 @@ func resolveReferencedSources(hasMultipleSources bool, source *v1alpha1.Applicat
 		return repoRefs, nil
 	}
 
-	for _, valueFile := range source.ValueFiles {
+	refFileParams := make([]string, 0)
+	for _, fileParam := range source.FileParameters {
+		refFileParams = append(refFileParams, fileParam.Path)
+	}
+	refCandidates := append(source.ValueFiles, refFileParams...)
+
+	for _, valueFile := range refCandidates {
 		if strings.HasPrefix(valueFile, "$") {
 			refVar := strings.Split(valueFile, "/")[0]
 
@@ -715,8 +721,14 @@ func (s *Service) runManifestGenAsync(ctx context.Context, repoRoot, commitSHA,
 		if q.HasMultipleSources {
 			if q.ApplicationSource.Helm != nil {
 
+				refFileParams := make([]string, 0)
+				for _, fileParam := range q.ApplicationSource.Helm.FileParameters {
+					refFileParams = append(refFileParams, fileParam.Path)
+				}
+				refCandidates := append(q.ApplicationSource.Helm.ValueFiles, refFileParams...)
+
 				// Checkout every one of the referenced sources to the target revision before generating Manifests
-				for _, valueFile := range q.ApplicationSource.Helm.ValueFiles {
+				for _, valueFile := range refCandidates {
 					if strings.HasPrefix(valueFile, "$") {
 						refVar := strings.Split(valueFile, "/")[0]
 
@@ -1168,9 +1180,19 @@ func helmTemplate(appPath string, repoRoot string, env *v1alpha1.Env, q *apiclie
 			}
 		}
 		for _, p := range appHelm.FileParameters {
-			resolvedPath, _, err := pathutil.ResolveValueFilePathOrUrl(appPath, repoRoot, env.Envsubst(p.Path), q.GetValuesFileSchemes())
-			if err != nil {
-				return nil, fmt.Errorf("error resolving helm value file path: %w", err)
+			var resolvedPath pathutil.ResolvedFilePath
+			referencedSource := getReferencedSource(p.Path, q.RefSources)
+			if referencedSource != nil {
+				// If the $-prefixed path appears to reference another source, do env substituion _after_ resolving the source
+				resolvedPath, err = getResolvedRefValueFile(p.Path, env, q.GetValuesFileSchemes(), referencedSource.Repo.Repo, gitRepoPaths)
+				if err != nil {
+					return nil, fmt.Errorf("error resolving set-file path: %w", err)
+				}
+			} else {
+				resolvedPath, _, err = pathutil.ResolveValueFilePathOrUrl(appPath, repoRoot, env.Envsubst(p.Path), q.GetValuesFileSchemes())
+				if err != nil {
+					return nil, fmt.Errorf("error resolving helm value file path: %w", err)
+				}
 			}
 			templateOpts.SetFile[p.Name] = resolvedPath
 		}
diff --git a/reposerver/repository/repository_test.go b/reposerver/repository/repository_test.go
index f99ce611777c2..90ab5cdf09fca 100644
--- a/reposerver/repository/repository_test.go
+++ b/reposerver/repository/repository_test.go
@@ -2208,6 +2208,44 @@ func TestGenerateManifestWithAnnotatedTagsAndMultiSourceApp(t *testing.T) {
 	}
 }
 
+func TestGenerateMultiSourceHelmWithFileParameter(t *testing.T) {
+
+	service := newService(t, "../../util/helm/testdata")
+
+	refSources := map[string]*argoappv1.RefTarget{}
+
+	refSources["$global"] = &argoappv1.RefTarget{
+		TargetRevision: "HEAD",
+	}
+
+	manifestRequest := &apiclient.ManifestRequest{
+		Repo: &argoappv1.Repository{},
+		ApplicationSource: &argoappv1.ApplicationSource{
+			Ref:            "$global",
+			Path:           "./redis",
+			TargetRevision: "HEAD",
+			Helm: &argoappv1.ApplicationSourceHelm{
+				ValueFiles: []string{"$global/redis/values-production.yaml"},
+				FileParameters: []argoappv1.HelmFileParameter{{
+					Name: "password",
+					Path: "$global/external/external-secret.txt",
+				}},
+			},
+		},
+		HasMultipleSources: true,
+		NoCache:            true,
+		RefSources:         refSources,
+	}
+
+	res, err := service.GenerateManifest(context.Background(), manifestRequest)
+	if err != nil {
+		t.Errorf("unexpected %s", err)
+	}
+
+	assert.NoError(t, err)
+	assert.Contains(t, res.Manifests[6], `"replicas":3`, "Values should not be overriden")
+}
+
 func TestFindResources(t *testing.T) {
 	testCases := []struct {
 		name          string