diff --git a/scripts/upgrade b/scripts/upgrade
index 19e4232..ccc78e5 100644
--- a/scripts/upgrade
+++ b/scripts/upgrade
@@ -38,7 +38,9 @@ then
 	ynh_script_progression --message="Upgrading source files..." --weight=20
 
 	# Download, check integrity, uncompress and patch the source from app.src
-	ynh_setup_source --dest_dir="$install_dir" --full_replace=1
+	# The keep option prevents this warning:
+	#   "File .... has been manually modified since the installation or last upgrade."
+	ynh_setup_source --dest_dir="$install_dir" --full_replace=1 --keep="config/elasticsearch.yml"
 fi
 
 chmod -R o-rwx "$install_dir"