diff --git a/scripts/upgrade b/scripts/upgrade
index e268d2d..3edf134 100644
--- a/scripts/upgrade
+++ b/scripts/upgrade
@@ -86,6 +86,12 @@ ynh_app_setting_set --app=$app --key=discovery_client --value=$discovery_client
 #=================================================
 ynh_script_progression --message="Upgrading packages..." --weight=3
 
+# Backup the configuration files to prevent yunohost to see a manual edit
+bakdir=$(mktemp -d)
+for name in system.xml network.xml logging.json; do
+	cp "$config_path/$name" "$bakdir/$name"
+done
+
 # ynh_package_install passes --no-remove so the ffmpeg5 -> ffmpeg6 migration is blocked.
 # So we remove the packages before installing the new ones.
 if ynh_package_is_installed "jellyfin-ffmpeg5"; then
@@ -111,6 +117,12 @@ ynh_add_nginx_config
 #=================================================
 ynh_script_progression --message="Updating a configuration file..." --weight=2
 
+# Restore the files we just backed up before installing the debs...
+for name in system.xml network.xml logging.json; do
+	mv -f "$bakdir/$name" "$config_path/$name"
+done
+ynh_secure_remove "$bakdir"
+
 # TODO: investigate if we can avoid overriding system.xml
 #ynh_add_config --template="system.xml" --destination="$config_path/system.xml"
 ynh_add_config --template="network.xml" --destination="$config_path/network.xml"