diff --git a/data/hooks/conf_regen/01-yunohost b/data/hooks/conf_regen/01-yunohost
index f699f105c..abc6f3780 100755
--- a/data/hooks/conf_regen/01-yunohost
+++ b/data/hooks/conf_regen/01-yunohost
@@ -63,6 +63,10 @@ SHELL=/bin/bash
 0 7,19 * * * root : YunoHost Automatic Diagnosis; sleep \$((RANDOM\\%1200)); yunohost diagnosis run --email > /dev/null 2>/dev/null || echo "Running the automatic diagnosis failed miserably"
 EOF
 
+  # legacy stuff to avoid yunohost reporting etckeeper as manually modified
+  # (this make sure that the hash is null / file is flagged as to-delete)
+  mkdir -p $pending_dir/etc/etckeeper
+  touch $pending_dir/etc/etckeeper/etckeeper.conf
 }
 
 do_post_regen() {