diff --git a/lib/mix/lib/mix/scm/git.ex b/lib/mix/lib/mix/scm/git.ex
index e59c6c29826..cb2c29f5c35 100644
--- a/lib/mix/lib/mix/scm/git.ex
+++ b/lib/mix/lib/mix/scm/git.ex
@@ -141,7 +141,7 @@ defmodule Mix.SCM.Git do
 
     # Migrate the Git repo
     rev = lock_rev || get_origin_opts_rev(opts) || default_branch()
-    git!(["--git-dir=.git", "checkout", "--quiet", rev])
+    git!(["--git-dir=.git", "checkout", "--force", "--quiet", rev])
 
     if opts[:submodules] do
       git!(~w[-c core.hooksPath='' --git-dir=.git submodule update --init --recursive])
diff --git a/lib/mix/test/mix/tasks/deps.git_test.exs b/lib/mix/test/mix/tasks/deps.git_test.exs
index 42559acb7cc..c2e97ffc4f4 100644
--- a/lib/mix/test/mix/tasks/deps.git_test.exs
+++ b/lib/mix/test/mix/tasks/deps.git_test.exs
@@ -400,9 +400,14 @@ defmodule Mix.Tasks.DepsGitTest do
       Mix.State.clear_cache()
       purge([DepsOnGitRepo.MixProject])
 
+      # Write to the checkout location to ensure it is replaced
+      File.mkdir_p!("deps/deps_on_git_repo/lib")
+      File.write!("deps/deps_on_git_repo/lib/deps_on_git_repo.ex", "# WILL BE OVERRIDDEN")
+
       Mix.Tasks.Deps.Update.run(["deps_on_git_repo"])
       assert File.exists?("deps/git_repo/lib/git_repo.ex")
       assert File.read!("mix.lock") =~ last
+      assert File.read!("deps/deps_on_git_repo/lib/deps_on_git_repo.ex") =~ "GitRepo.hello()"
       refute File.exists?("_build/dev/lib/git_repo/.mix/compile.fetch")
     end)
   after
@@ -427,10 +432,15 @@ defmodule Mix.Tasks.DepsGitTest do
       Mix.State.clear_cache()
       purge([DepsOnGitRepo.MixProject])
 
+      # Write to the checkout location to ensure it is replaced
+      File.mkdir_p!("deps/deps_on_git_repo/lib")
+      File.write!("deps/deps_on_git_repo/lib/deps_on_git_repo.ex", "# WILL BE OVERRIDDEN")
+
       Mix.Dep.Lock.write(%{deps_on_git_repo: {:git, fixture_path("deps_on_git_repo"), last, []}})
       Mix.Tasks.Deps.Get.run([])
       assert File.exists?("deps/git_repo/lib/git_repo.ex")
       assert File.read!("mix.lock") =~ last
+      assert File.read!("deps/deps_on_git_repo/lib/deps_on_git_repo.ex") =~ "GitRepo.hello()"
       refute File.exists?("_build/dev/lib/git_repo/.mix/compile.fetch")
     end)
   after