diff --git a/GVFS/GVFS.FunctionalTests/Tools/ControlGitRepo.cs b/GVFS/GVFS.FunctionalTests/Tools/ControlGitRepo.cs
index d2f792cea..e8c40099d 100644
--- a/GVFS/GVFS.FunctionalTests/Tools/ControlGitRepo.cs
+++ b/GVFS/GVFS.FunctionalTests/Tools/ControlGitRepo.cs
@@ -66,6 +66,9 @@ public void Initialize()
             GitProcess.Invoke(this.RootPath, "branch --set-upstream " + this.Commitish + " origin/" + this.Commitish);
             GitProcess.Invoke(this.RootPath, "checkout " + this.Commitish);
             GitProcess.Invoke(this.RootPath, "branch --unset-upstream");
+
+            // Enable the ORT merge strategy
+            GitProcess.Invoke(this.RootPath, "config pull.twohead ort");
         }
 
         public void Fetch(string commitish)