diff --git a/internal/manager/manager.go b/internal/manager/manager.go
index 79db2bb30..554d36cf9 100644
--- a/internal/manager/manager.go
+++ b/internal/manager/manager.go
@@ -586,18 +586,25 @@ func (s *Manager) Setup(ctx context.Context, input SetupInput) error {
 	// create the config directory if it does not exist
 	// don't do anything if config is already set in the environment
 	if !config.FileEnvSet() {
-		configDir := filepath.Dir(input.ConfigLocation)
+		// #3304 - if config path is relative, it breaks the ffmpeg/ffprobe
+		// paths since they must not be relative. The config file property is
+		// resolved to an absolute path when stash is run normally, so convert
+		// relative paths to absolute paths during setup.
+		configFile, _ := filepath.Abs(input.ConfigLocation)
+
+		configDir := filepath.Dir(configFile)
+
 		if exists, _ := fsutil.DirExists(configDir); !exists {
 			if err := os.Mkdir(configDir, 0755); err != nil {
 				return fmt.Errorf("error creating config directory: %v", err)
 			}
 		}
 
-		if err := fsutil.Touch(input.ConfigLocation); err != nil {
+		if err := fsutil.Touch(configFile); err != nil {
 			return fmt.Errorf("error creating config file: %v", err)
 		}
 
-		s.Config.SetConfigFile(input.ConfigLocation)
+		s.Config.SetConfigFile(configFile)
 	}
 
 	// create the generated directory if it does not exist