diff --git a/pkg/helm/v3/dependency.go b/pkg/helm/v3/dependency.go
index 423f00f05..8a535b3ff 100644
--- a/pkg/helm/v3/dependency.go
+++ b/pkg/helm/v3/dependency.go
@@ -1,12 +1,22 @@
 package v3
 
 import (
+	"os"
+	"path/filepath"
+	"strings"
+	"time"
+
 	"helm.sh/helm/v3/pkg/downloader"
 
 	"github.com/fluxcd/helm-operator/pkg/utils"
 )
 
 func (h *HelmV3) DependencyUpdate(chartPath string) error {
+	// Garbage collect before the dependency update so that
+	// anonymous files from previous runs are cleared, with
+	// a safe guard time offset to not touch any files in
+	// use.
+	garbageCollect(repositoryCache, time.Second * 120)
 	out := utils.NewLogWriter(h.logger)
 	man := &downloader.Manager{
 		Out:              out,
@@ -17,3 +27,22 @@ func (h *HelmV3) DependencyUpdate(chartPath string) error {
 	}
 	return man.Update()
 }
+
+// garbageCollect walks over the files in the given path and deletes
+// any anonymous index file with a mod time older than the given
+// duration.
+func garbageCollect(path string, olderThan time.Duration) {
+	now := time.Now()
+	filepath.Walk(path, func(p string, f os.FileInfo, err error) error {
+		if err != nil || f.IsDir() {
+			return nil
+		}
+		if strings.HasSuffix(f.Name(), "=-index.yaml") || strings.HasSuffix(f.Name(), "=-charts.txt") {
+			if diff := now.Sub(f.ModTime()); diff > olderThan {
+				return os.Remove(p)
+			}
+			return nil
+		}
+		return nil
+	})
+}