diff --git a/docs/user-guide/helm.md b/docs/user-guide/helm.md
index 3b5a5de0dc262..455e682e33bab 100644
--- a/docs/user-guide/helm.md
+++ b/docs/user-guide/helm.md
@@ -236,9 +236,6 @@ 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)
-
 ## Helm Release Name
 
 By default, the Helm release name is equal to the Application name to which it belongs. Sometimes, especially on a centralised Argo CD,
diff --git a/reposerver/repository/repository.go b/reposerver/repository/repository.go
index 9356f2d0062c7..d23bdab80cad9 100644
--- a/reposerver/repository/repository.go
+++ b/reposerver/repository/repository.go
@@ -472,7 +472,13 @@ 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]
 
@@ -710,8 +716,14 @@ func (s *Service) runManifestGenAsync(ctx context.Context, repoRoot, commitSHA,
 		// check whether they should be replicated in resolveReferencedSources.
 		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]
 
@@ -1158,9 +1170,19 @@ 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 substitution _after_ resolving the source
+				resolvedPath, err = getResolvedRefValueFile(p.Path, env, q.GetValuesFileSchemes(), referencedSource.Repo.Repo, gitRepoPaths, referencedSource.Repo.Project)
+				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 06177b28a1d83..69e051a87f5e1 100644
--- a/reposerver/repository/repository_test.go
+++ b/reposerver/repository/repository_test.go
@@ -13,6 +13,7 @@ import (
 	"path"
 	"path/filepath"
 	"regexp"
+	"slices"
 	"sort"
 	"strings"
 	"sync"
@@ -2228,6 +2229,72 @@ func TestGenerateManifestWithAnnotatedTagsAndMultiSourceApp(t *testing.T) {
 	}
 }
 
+func TestGenerateMultiSourceHelmWithFileParameter(t *testing.T) {
+	expectedFileContent, err := os.ReadFile("../../util/helm/testdata/external/external-secret.txt")
+	assert.NoError(t, err)
+
+	service := newService(t, "../../util/helm/testdata")
+
+	testCases := []struct {
+		name            string
+		refSources      map[string]*argoappv1.RefTarget
+		expectedContent string
+		expectedErr     bool
+	}{{
+		name: "Successfully resolve multi-source ref for helm set-file",
+		refSources: map[string]*argoappv1.RefTarget{
+			"$global": {
+				TargetRevision: "HEAD",
+			},
+		},
+		expectedContent: string(expectedFileContent),
+		expectedErr:     false,
+	}, {
+		name:            "Failed to resolve multi-source ref for helm set-file",
+		refSources:      map[string]*argoappv1.RefTarget{},
+		expectedContent: "DOES-NOT-EXIST",
+		expectedErr:     true,
+	}}
+
+	for i := range testCases {
+		tc := testCases[i]
+		t.Run(tc.name, func(t *testing.T) {
+			manifestRequest := &apiclient.ManifestRequest{
+				Repo: &argoappv1.Repository{},
+				ApplicationSource: &argoappv1.ApplicationSource{
+					Ref:            "$global",
+					Path:           "./redis",
+					TargetRevision: "HEAD",
+					Helm: &argoappv1.ApplicationSourceHelm{
+						ValueFiles: []string{"$global/redis/values-production.yaml"},
+						FileParameters: []argoappv1.HelmFileParameter{{
+							Name: "passwordContent",
+							Path: "$global/external/external-secret.txt",
+						}},
+					},
+				},
+				HasMultipleSources: true,
+				NoCache:            true,
+				RefSources:         tc.refSources,
+			}
+
+			res, err := service.GenerateManifest(context.Background(), manifestRequest)
+
+			if !tc.expectedErr {
+				assert.NoError(t, err)
+
+				// Check that any of the manifests contains the secret
+				idx := slices.IndexFunc(res.Manifests, func(content string) bool {
+					return strings.Contains(content, tc.expectedContent)
+				})
+				assert.GreaterOrEqual(t, idx, 0, "No manifest contains the value set with the helm fileParameters")
+			} else {
+				assert.Error(t, err)
+			}
+		})
+	}
+}
+
 func TestFindResources(t *testing.T) {
 	testCases := []struct {
 		name          string