diff --git a/src/lib/Hydra/Plugin/GitInput.pm b/src/lib/Hydra/Plugin/GitInput.pm
index 53f373d0..8c02de7e 100644
--- a/src/lib/Hydra/Plugin/GitInput.pm
+++ b/src/lib/Hydra/Plugin/GitInput.pm
@@ -40,7 +40,7 @@ sub _cloneRepo {
     if (defined $deepClone) {
 
         # Checkout the branch to look at its content.
-        $res = run(cmd => ["git", "checkout", "$branch"], dir => $clonePath);
+        $res = run(cmd => ["git", "checkout", "--force", "$branch"], dir => $clonePath);
         die "error checking out Git branch '$branch' at `$uri':\n$res->{stderr}" if $res->{status};
 
         if (-f ".topdeps") {