diff --git a/yadm b/yadm
index f07a649..a326d8f 100755
--- a/yadm
+++ b/yadm
@@ -771,7 +771,7 @@ function clone() {
   configure_repo
 
   # then reset the index as the --no-checkout flag makes the index empty
-  "$GIT_PROGRAM" reset --quiet -- .
+  "$GIT_PROGRAM" reset --quiet -- "$YADM_WORK"
 
   if [ "$YADM_WORK" = "$HOME" ]; then
     debug "Determining if repo tracks private directories"