diff --git a/scripts/upgrade b/scripts/upgrade
index 73c534f..fe23a1f 100644
--- a/scripts/upgrade
+++ b/scripts/upgrade
@@ -29,14 +29,6 @@ if [ -z "${secret_key:-}" ]; then
 	ynh_app_setting_set --app=$app --key=secret_key --value=$secret_key
 fi
 
-if [ -d "$install_dir/data" ]; then
-    ynh_print_warn "Migrating data directory to $data_dir..."
-
-    # remove old configuration files
-	ynh_secure_remove --file="$install_dir/data/config.local.user.php"
-	mv "$install_dir/data" "$data_dir"
-fi
-
 #=================================================
 # DOWNLOAD, CHECK AND UNPACK SOURCE
 #=================================================
@@ -44,12 +36,21 @@ fi
 if [ "$upgrade_type" == "UPGRADE_APP" ]
 then
 	ynh_script_progression --message="Upgrading source files..." --weight=5
+
+	if [ -d "$install_dir/data" ]; then
+    	ynh_print_warn "Migrating data directory to $data_dir..."
+
+    	# remove old configuration files
+		ynh_secure_remove --file="$install_dir/data/config.local.user.php"
+		mv "$install_dir/data" "$data_dir"
+	fi
+
+	ynh_secure_remove --file="$install_dir/config.local.yunohost.php"
+	
 	# Download, check integrity, uncompress and patch the source from app.src
 	ynh_setup_source --dest_dir="$install_dir" #--keep="config.local.php"
 fi
 
-ynh_secure_remove --file="$install_dir/config.local.yunohost.php"
-
 chmod -R o-rwx "$install_dir"
 chown -R $app:www-data "$install_dir"