diff --git a/pkg/apk/apk/cache.go b/pkg/apk/apk/cache.go
index 78ce1097a..1d28e666e 100644
--- a/pkg/apk/apk/cache.go
+++ b/pkg/apk/apk/cache.go
@@ -492,16 +492,16 @@ func cachePathFromURL(root string, u url.URL) (string, error) {
 	u2.ForceQuery = false
 	u2.RawFragment = ""
 	u2.RawQuery = ""
-	filename := filepath.Base(u2.Path)
-	archDir := filepath.Dir(u2.Path)
-	dir := filepath.Base(archDir)
-	repoDir := filepath.Dir(archDir)
-	// include the hostname
-	u2.Path = repoDir
-
-	// url encode it so it can be a single directory
-	repoDir = url.QueryEscape(u2.String())
-	cacheFile := filepath.Join(root, repoDir, dir, filename)
+
+	// Use the full path as the cache structure to handle both top-level and nested files uniformly
+	cachePath := strings.TrimPrefix(filepath.Clean(u2.Path), "/")
+	baseURL := u2
+	baseURL.Path = ""
+
+	// url encode the base URL so it can be a single directory
+	baseDir := url.QueryEscape(baseURL.String())
+	cacheFile := filepath.Join(root, baseDir, cachePath)
+
 	// validate it is within root
 	cacheFile = filepath.Clean(cacheFile)
 	cleanroot := filepath.Clean(root)
diff --git a/pkg/apk/apk/implementation_test.go b/pkg/apk/apk/implementation_test.go
index 163098b9d..dfdd184c4 100644
--- a/pkg/apk/apk/implementation_test.go
+++ b/pkg/apk/apk/implementation_test.go
@@ -715,7 +715,10 @@ func TestFetchPackage(t *testing.T) {
 		tmpDir := t.TempDir()
 		a := prepLayout(t, tmpDir)
 		// fill the cache
-		repoDir := filepath.Join(tmpDir, url.QueryEscape(testAlpineRepos), testArch)
+		// New cache structure uses full path: https%3A%2F%2Fhost/path/to/arch/file
+		repoURL, _ := url.Parse(testAlpineRepos)
+		baseDir := url.QueryEscape(repoURL.Scheme + "://" + repoURL.Host)
+		repoDir := filepath.Join(tmpDir, baseDir, strings.TrimPrefix(repoURL.Path, "/"), testArch)
 		err := os.MkdirAll(repoDir, 0o755)
 		require.NoError(t, err, "unable to mkdir cache")
 
@@ -757,7 +760,9 @@ func TestFetchPackage(t *testing.T) {
 		tmpDir := t.TempDir()
 		a := prepLayout(t, tmpDir)
 		// fill the cache
-		repoDir := filepath.Join(tmpDir, url.QueryEscape(testAlpineRepos), testArch)
+		repoURL, _ := url.Parse(testAlpineRepos)
+		baseDir := url.QueryEscape(repoURL.Scheme + "://" + repoURL.Host)
+		repoDir := filepath.Join(tmpDir, baseDir, strings.TrimPrefix(repoURL.Path, "/"), testArch)
 		err := os.MkdirAll(repoDir, 0o755)
 		require.NoError(t, err, "unable to mkdir cache")
 
@@ -785,7 +790,9 @@ func TestFetchPackage(t *testing.T) {
 		tmpDir := t.TempDir()
 		a := prepLayout(t, tmpDir)
 		// fill the cache
-		repoDir := filepath.Join(tmpDir, url.QueryEscape(testAlpineRepos), testArch)
+		repoURL, _ := url.Parse(testAlpineRepos)
+		baseDir := url.QueryEscape(repoURL.Scheme + "://" + repoURL.Host)
+		repoDir := filepath.Join(tmpDir, baseDir, strings.TrimPrefix(repoURL.Path, "/"), testArch)
 		err := os.MkdirAll(repoDir, 0o755)
 		require.NoError(t, err, "unable to mkdir cache")
 
@@ -815,7 +822,9 @@ func TestFetchPackage(t *testing.T) {
 		tmpDir := t.TempDir()
 		a := prepLayout(t, tmpDir)
 		// fill the cache
-		repoDir := filepath.Join(tmpDir, url.QueryEscape(testAlpineRepos), testArch)
+		repoURL, _ := url.Parse(testAlpineRepos)
+		baseDir := url.QueryEscape(repoURL.Scheme + "://" + repoURL.Host)
+		repoDir := filepath.Join(tmpDir, baseDir, strings.TrimPrefix(repoURL.Path, "/"), testArch)
 		err := os.MkdirAll(repoDir, 0o755)
 		require.NoError(t, err, "unable to mkdir cache")
 
diff --git a/pkg/apk/apk/repo_test.go b/pkg/apk/apk/repo_test.go
index 7dae913cc..eb0fc109f 100644
--- a/pkg/apk/apk/repo_test.go
+++ b/pkg/apk/apk/repo_test.go
@@ -178,7 +178,9 @@ func TestGetRepositoryIndexes(t *testing.T) {
 		tmpDir := t.TempDir()
 		a := prepLayout(t, tmpDir, []string{testAlpineRepos})
 		// fill the cache
-		repoDir := filepath.Join(tmpDir, url.QueryEscape(testAlpineRepos), testArch)
+		repoURL, _ := url.Parse(testAlpineRepos)
+		baseDir := url.QueryEscape(repoURL.Scheme + "://" + repoURL.Host)
+		repoDir := filepath.Join(tmpDir, baseDir, strings.TrimPrefix(repoURL.Path, "/"), testArch)
 
 		a.SetClient(&http.Client{
 			Transport: &testLocalTransport{