diff --git a/internal/config/config.go b/internal/config/config.go
index 9d1bf4f..34652ec 100644
--- a/internal/config/config.go
+++ b/internal/config/config.go
@@ -275,7 +275,8 @@ func getUnusedDirs(apps map[string]App) (map[string]struct{}, error) {
 	unusedDirs := make(map[string]struct{})
 	for _, file := range files {
 		// Ignore config file
-		if file.Name() == configFileJSON {
+		if file.Name() == configFileJSON ||
+			file.Name() == configFileTOML {
 			continue
 		}