diff --git a/plugins/git/functions b/plugins/git/functions
index c98efab1b..152360eac 100755
--- a/plugins/git/functions
+++ b/plugins/git/functions
@@ -64,6 +64,12 @@ git_build_app_repo() {
   suppress_output git submodule update --init --recursive
   find . -name .git -prune -exec rm -rf {} \; > /dev/null
 
+  if use_git_worktree; then
+    pushd "$DOKKU_ROOT/$APP"
+    git worktree prune
+    popd
+  fi
+
   local DOKKU_APP_DISABLE_ANSI_PREFIX_REMOVAL DOKKU_GLOBAL_DISABLE_ANSI_PREFIX_REMOVAL DOKKU_DISABLE_ANSI_PREFIX_REMOVAL
   DOKKU_APP_DISABLE_ANSI_PREFIX_REMOVAL=$(config_get "$APP" DOKKU_DISABLE_ANSI_PREFIX_REMOVAL || true)
   DOKKU_GLOBAL_DISABLE_ANSI_PREFIX_REMOVAL=$(config_get --global DOKKU_DISABLE_ANSI_PREFIX_REMOVAL || true)