diff --git a/scripts/upgrade b/scripts/upgrade
index 79bd061..e39d226 100644
--- a/scripts/upgrade
+++ b/scripts/upgrade
@@ -115,8 +115,16 @@ if [ "$upgrade_type" == "UPGRADE_APP" ]
 then
 	ynh_print_info --message="Upgrading source files..."
 
+	config_file="$final_path/config.yml"
+	tmpdir="$(mktemp -d)"
+
+	rsync -a "$config_file" "$tmpdir/."
+	ynh_secure_remove --file="$final_path"
+
 	# Download, check integrity, uncompress and patch the source from app.src
 	ynh_setup_source --dest_dir="$final_path"
+
+	rsync -a "$tmpdir/config.yml" "$final_path/."
 fi
 
 #=================================================