diff --git a/test/test_init.py b/test/test_init.py
index c738a02..177b907 100644
--- a/test/test_init.py
+++ b/test/test_init.py
@@ -60,10 +60,11 @@ def test_init(
     else:
         assert run.success
         assert 'Initialized empty shared Git repository' in run.out
-        assert run.err == ''
 
         if repo_present:
             assert not old_repo.isfile(), 'Original repo still exists'
+        else:
+            assert run.err == ''
 
         if alt_work:
             assert repo_config('core.worktree') == paths.work
diff --git a/yadm b/yadm
index e374329..6af23e8 100755
--- a/yadm
+++ b/yadm
@@ -747,6 +747,7 @@ function clone() {
   # remove existing if forcing the clone to happen anyway
   [ -d "$YADM_REPO" ] && {
     debug "Removing existing repo prior to clone"
+    "$GIT_PROGRAM" -C "$YADM_WORK" submodule deinit -f --all
     rm -rf "$YADM_REPO"
   }
 
@@ -1129,6 +1130,7 @@ function init() {
   # remove existing if forcing the init to happen anyway
   [ -d "$YADM_REPO" ] && {
     debug "Removing existing repo prior to init"
+    "$GIT_PROGRAM" -C "$YADM_WORK" submodule deinit -f --all
     rm -rf "$YADM_REPO"
   }