If GitLab CI is configured to utilize **git fetch** instead of **git clone** it will not clean out any subdirectory containing a **.git** directory. From **git help clean** http://git-scm.com/docs/git-clean#_options : > -f > [...] Git will refuse to delete directories with .git sub directory or file unless a second -f is given. [...] How git clean is utilized right now (in shells/{cmd,bash,powershell}.go) is: **git clean -fdx** I suggest to change it to: **git clean -ffdx** to make subdirectories containing git repositories being cleaned out by default.