diff --git a/internal/gps/prune.go b/internal/gps/prune.go
index 4273f3eba8..4b74265a8b 100644
--- a/internal/gps/prune.go
+++ b/internal/gps/prune.go
@@ -45,6 +45,10 @@ func Prune(baseDir string, l Lock, options PruneOptions, logger *log.Logger) err
 		}
 	}
 
+	if err := pruneEmptyDirs(baseDir, logger); err != nil {
+		return errors.Wrap(err, "could not prune empty dirs")
+	}
+
 	if (options & PruneUnusedPackages) != 0 {
 		if l == nil {
 			return errors.New("pruning unused packages requires passing non-nil Lock")
@@ -54,17 +58,17 @@ func Prune(baseDir string, l Lock, options PruneOptions, logger *log.Logger) err
 		}
 	}
 
-	// if (options & PruneNonGoFiles) != 0 {
-	// 	if err := pruneNonGoFiles(baseDir, logger); err != nil {
-	// 		return err
-	// 	}
-	// }
+	if (options & PruneNonGoFiles) != 0 {
+		if err := pruneNonGoFiles(baseDir, logger); err != nil {
+			return err
+		}
+	}
 
-	// if (options & PruneGoTestFiles) != 0 {
-	// 	if err := pruneGoTestFiles(baseDir, logger); err != nil {
-	// 		return err
-	// 	}
-	// }
+	if (options & PruneGoTestFiles) != 0 {
+		if err := pruneGoTestFiles(baseDir, logger); err != nil {
+			return err
+		}
+	}
 
 	// Delete all empty directories.
 	return errors.Wrap(pruneEmptyDirs(baseDir, logger), "could not prune empty dirs")
@@ -85,7 +89,9 @@ func pruneUnusedPackages(baseDir string, l Lock, logger *log.Logger) error {
 
 		files, err := ioutil.ReadDir(pkgPath)
 		if err != nil {
-			return err
+			// TODO(ibrasho) Handle this error properly.
+			// It happens when attempting to ioutil.ReadDir a submodule.
+			continue
 		}
 
 		// Delete *.go files in the package directory.
@@ -267,6 +273,8 @@ func pruneEmptyDirs(baseDir string, logger *log.Logger) error {
 		if logger != nil {
 			logger.Printf("  %s\n", strings.TrimPrefix(dir, baseDir+string(os.PathSeparator)))
 		}
+	}
+	for _, dir := range empty {
 		if err := os.Remove(dir); err != nil {
 			return err
 		}