diff --git a/scripts/upgrade b/scripts/upgrade
index d2a3103..a693c39 100644
--- a/scripts/upgrade
+++ b/scripts/upgrade
@@ -61,8 +61,23 @@ if [ "$upgrade_type" == "UPGRADE_APP" ]
 then
 	ynh_script_progression --message="Upgrading source files..." --weight=1
 
+	# Create a temporary directory
+  	tmpdir="$(mktemp -d)"
+
+    # Backup the config file in the temp dir
+  	cp -a "$final_path/.env" "$tmpdir/.env"
+
+	# Remove the app directory securely
+	ynh_secure_remove --file="$final_path"
+
 	# Download, check integrity, uncompress and patch the source from app.src
-	ynh_setup_source --dest_dir="$final_path" --keep="$final_path/.env"
+	ynh_setup_source --dest_dir="$final_path"
+
+	# Copy the admin saved settings from tmp directory to final path  
+  	cp -a "$tmpdir/.env" "$final_path/.env" 
+
+  	# Remove the tmp directory securely
+  	ynh_secure_remove --file="$tmpdir"
 fi
 
 #=================================================