diff --git a/helpers/utils b/helpers/utils
index 8b28000d6..edbdbdc3a 100644
--- a/helpers/utils
+++ b/helpers/utils
@@ -374,7 +374,13 @@ ynh_setup_source() {
         for stuff_to_keep in $keep; do
             if [ -e "$keep_dir/$stuff_to_keep" ]; then
                 mkdir --parents "$(dirname "$dest_dir/$stuff_to_keep")"
-                cp --archive "$keep_dir/$stuff_to_keep" "$dest_dir/$stuff_to_keep"
+
+                # We add "--no-target-directory" (short option is -T) to handle the special case
+                # when we "keep" a folder, but then the new setup already contains the same dir (but possibly empty)
+                # in which case a regular "cp" will create a copy of the directory inside the directory ...
+                # resulting in something like /var/www/$app/data/data instead of /var/www/$app/data
+                # cf https://unix.stackexchange.com/q/94831 for a more elaborate explanation on the option
+                cp --archive --no-target-directory "$keep_dir/$stuff_to_keep" "$dest_dir/$stuff_to_keep"
             fi
         done
     fi