diff --git a/docs/deployment/methods/git.md b/docs/deployment/methods/git.md
index 061c3c926..564e7425e 100644
--- a/docs/deployment/methods/git.md
+++ b/docs/deployment/methods/git.md
@@ -109,6 +109,8 @@ dokku git:set node-js-app keep-git-dir false
 dokku git:set node-js-app keep-git-dir ""
 ```
 
+Please keep in mind that setting `keep-git-dir` to `true` may result in unstaged changes shown within the built container due to the build process generating application changes within the built app directory.
+
 ### Initializing an app repository from a remote repository
 
 > The application must exist before the repository can be initialized
diff --git a/plugins/git/functions b/plugins/git/functions
index 450685c1a..114c28971 100755
--- a/plugins/git/functions
+++ b/plugins/git/functions
@@ -9,19 +9,10 @@ set -eo pipefail
 
 use_git_worktree() {
   declare desc="detects whether to use git worktree"
-  local GIT_VERSION MAJOR_VERSION MINOR_VERSION
+  declare deprecated=true
+  dokku_log_warn "Deprecated: fn-git-use-worktree"
 
-  GIT_VERSION=$(git --version | awk '{split($0,a," "); print a[3]}')
-  MAJOR_VERSION=$(echo "$GIT_VERSION" | awk '{split($0,a,"."); print a[1]}')
-  MINOR_VERSION=$(echo "$GIT_VERSION" | awk '{split($0,a,"."); print a[2]}')
-
-  if [[ "$MAJOR_VERSION" -ge "3" ]]; then
-    return 0
-  elif [[ "$MAJOR_VERSION" -eq "2" ]] && [[ "$MINOR_VERSION" -ge "11" ]]; then
-    return 0
-  else
-    return 1
-  fi
+  fn-git-use-worktree
 }
 
 git_build_app_repo() {
@@ -35,49 +26,13 @@ git_build_app_repo() {
   local GIT_BUILD_APP_REPO_TMP_WORK_DIR=$(mktemp -d "/tmp/dokku-${DOKKU_PID}-${FUNCNAME[0]}.XXXXXX")
   trap "rm -rf '$GIT_BUILD_APP_REPO_TMP_WORK_DIR' >/dev/null" RETURN INT TERM EXIT
 
-  local TMP_TAG="dokku/$REV"
   chmod 755 "$GIT_BUILD_APP_REPO_TMP_WORK_DIR"
-  unset GIT_DIR GIT_WORK_TREE
+  unset GIT_DIR GIT_QUARANTINE_PATH GIT_WORK_TREE
 
   ! plugn trigger app-exists "$APP" >/dev/null 2>&1 && plugn trigger app-maybe-create "$APP"
 
-  if use_git_worktree; then
-    # git worktree - this method uses git worktree which was introduced in git 2.5
-    pushd "$DOKKU_ROOT/$APP" >/dev/null
-    # unset the git quarantine path to allow us to use 2.13.0+
-    # See this issue for more information: https://github.com/dokku/dokku/issues/2796
-    suppress_output env -u GIT_QUARANTINE_PATH git worktree add "$GIT_BUILD_APP_REPO_TMP_WORK_DIR" "$REV"
-    popd >/dev/null 2>&1 || pushd "/tmp" >/dev/null
-    pushd "$GIT_BUILD_APP_REPO_TMP_WORK_DIR" >/dev/null
-  else
-    # git clone - this method creates a new git repository and adds the primary
-    #             repo as a remote, then does a fetch depth=1 to avoid cloning
-    #             the entire repo.
-    #             Not working for git >= 2.11.0 due to changes introduced
-    #             in this merge:
-    #             https://github.com/git/git/commit/25ab004c53cdcfea485e5bf437aeaa74df47196d
-    pushd "$GIT_BUILD_APP_REPO_TMP_WORK_DIR" >/dev/null
-    GIT_DIR="$DOKKU_ROOT/$APP" git tag -d "$TMP_TAG" &>/dev/null || true
-    GIT_DIR="$DOKKU_ROOT/$APP" git tag "$TMP_TAG" "$REV" &>/dev/null
-    git init &>/dev/null
-    git config advice.detachedHead false
-    git remote add origin "$DOKKU_ROOT/$APP" &>/dev/null
-    git fetch --depth=1 origin "refs/tags/$TMP_TAG" &>/dev/null
-    git reset --hard FETCH_HEAD &>/dev/null
-    GIT_DIR="$DOKKU_ROOT/$APP" git tag -d "$TMP_TAG" &>/dev/null || true
-  fi
-
-  suppress_output env -u GIT_QUARANTINE_PATH git submodule update --init --recursive
-  local DOKKU_KEEP_GIT_DIR="$(fn-plugin-property-get "git" "$APP" "keep-git-dir" "")"
-  if [[ "$DOKKU_KEEP_GIT_DIR" != "true" ]]; then
-    find . -name .git -prune -exec rm -rf {} \; >/dev/null
-  fi
-
-  if use_git_worktree; then
-    pushd "$DOKKU_ROOT/$APP" >/dev/null
-    git worktree prune
-    popd >/dev/null
-  fi
+  fn-git-setup-build-dir "$APP" "$GIT_BUILD_APP_REPO_TMP_WORK_DIR" "$REV"
+  pushd "$GIT_BUILD_APP_REPO_TMP_WORK_DIR" >/dev/null
 
   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)
diff --git a/plugins/git/internal-functions b/plugins/git/internal-functions
index 74df9a476..8c781c8ae 100755
--- a/plugins/git/internal-functions
+++ b/plugins/git/internal-functions
@@ -257,3 +257,88 @@ fn-git-deploy-branch() {
     echo "$DEFAULT_BRANCH"
   fi
 }
+
+fn-git-setup-build-dir() {
+  declare APP="$1" GIT_WORKDIR="$2" REV="$3"
+  local DOKKU_KEEP_GIT_DIR="$(fn-plugin-property-get "git" "$APP" "keep-git-dir" "")"
+
+  if ! fn-git-use-worktree; then
+    fn-git-setup-build-dir-old "$APP" "$GIT_WORKDIR" "$REV"
+    return
+  fi
+
+  if [[ "$DOKKU_KEEP_GIT_DIR" == "true" ]]; then
+    fn-git-setup-build-dir-new "$APP" "$GIT_WORKDIR" "$REV"
+  else
+    fn-git-setup-build-dir-worktree "$APP" "$GIT_WORKDIR" "$REV"
+  fi
+}
+
+fn-git-setup-build-dir-new() {
+  declare APP="$1" GIT_WORKDIR="$2" REV="$3"
+  local DOKKU_DEPLOY_BRANCH="$(fn-git-deploy-branch "$APP")"
+
+  # repo workaround from https://gitlab.com/gitlab-org/gitlab-foss/-/issues/52249
+  # and https://docs.gitlab.com/ee/user/project/repository/repository_mirroring.html#preventing-conflicts-using-a-pre-receive-hook
+  env -u GIT_QUARANTINE_PATH git -C "$DOKKU_ROOT/$APP" archive "$REV" | tar x --warning=none -C "${GIT_WORKDIR}"
+  suppress_output env -u GIT_QUARANTINE_PATH git -C "$GIT_WORKDIR" clone --bare "$DOKKU_ROOT/$APP" .git
+  suppress_output env -u GIT_QUARANTINE_PATH git -C "$GIT_WORKDIR" config --local gc.auto 0
+  suppress_output env -u GIT_QUARANTINE_PATH git -C "$GIT_WORKDIR" config --local --bool core.bare false
+  suppress_output env -u GIT_QUARANTINE_PATH git -C "$GIT_WORKDIR" config --local receive.denyCurrentBranch ignore
+  suppress_output env -u GIT_QUARANTINE_PATH git -C "$GIT_WORKDIR" symbolic-ref HEAD "refs/heads/$DOKKU_DEPLOY_BRANCH"
+  suppress_output env -u GIT_QUARANTINE_PATH git -C "$GIT_WORKDIR" reset "$REV" -- .
+  suppress_output env -u GIT_QUARANTINE_PATH git -C "$GIT_WORKDIR" push $GIT_WORKDIR $REV:refs/heads/$DOKKU_DEPLOY_BRANCH
+  fn-git-setup-build-dir-submodules "$APP" "$GIT_WORKDIR"
+}
+
+fn-git-setup-build-dir-old() {
+  declare APP="$1" GIT_WORKDIR="$2" REV="$3"
+  local TMP_TAG="dokku/$REV"
+
+  suppress_output git -C "$DOKKU_ROOT/$APP" tag -d "$TMP_TAG" &>/dev/null || true
+  suppress_output git -C "$DOKKU_ROOT/$APP" tag "$TMP_TAG" "$REV"
+  suppress_output git -C "$GIT_WORKDIR" init
+  suppress_output git -C "$GIT_WORKDIR" config advice.detachedHead false
+  suppress_output git -C "$GIT_WORKDIR" remote add origin "$DOKKU_ROOT/$APP"
+  suppress_output git -C "$GIT_WORKDIR" fetch --depth=1 origin "refs/tags/$TMP_TAG"
+  suppress_output git -C "$GIT_WORKDIR" reset --hard FETCH_HEAD
+  suppress_output git -C "$DOKKU_ROOT/$APP" git tag -d "$TMP_TAG" &>/dev/null || true
+  fn-git-setup-build-dir-submodules "$APP" "$GIT_WORKDIR"
+}
+
+fn-git-setup-build-dir-worktree() {
+  declare APP="$1" GIT_WORKDIR="$2" REV="$3"
+
+  # unset the git quarantine path to allow us to use 2.13.0+
+  # See this issue for more information: https://github.com/dokku/dokku/issues/2796
+  suppress_output env -u GIT_QUARANTINE_PATH git -C "$DOKKU_ROOT/$APP" worktree add "$GIT_WORKDIR" "$REV"
+  fn-git-setup-build-dir-submodules "$APP" "$GIT_WORKDIR"
+  suppress_output git -C "$DOKKU_ROOT/$APP" worktree prune
+}
+
+fn-git-setup-build-dir-submodules() {
+  declare APP="$1" GIT_WORKDIR="$2"
+  local DOKKU_KEEP_GIT_DIR="$(fn-plugin-property-get "git" "$APP" "keep-git-dir" "")"
+
+  suppress_output env -u GIT_QUARANTINE_PATH git -C "$GIT_WORKDIR" submodule update --init --recursive
+  if [[ "$DOKKU_KEEP_GIT_DIR" != "true" ]]; then
+    find "$GIT_WORKDIR" -name .git -prune -exec rm -rf {} \; >/dev/null
+  fi
+}
+
+fn-git-use-worktree() {
+  declare desc="detects whether to use git worktree"
+  local GIT_VERSION MAJOR_VERSION MINOR_VERSION
+
+  GIT_VERSION=$(git --version | awk '{split($0,a," "); print a[3]}')
+  MAJOR_VERSION=$(echo "$GIT_VERSION" | awk '{split($0,a,"."); print a[1]}')
+  MINOR_VERSION=$(echo "$GIT_VERSION" | awk '{split($0,a,"."); print a[2]}')
+
+  if [[ "$MAJOR_VERSION" -ge "3" ]]; then
+    return 0
+  elif [[ "$MAJOR_VERSION" -eq "2" ]] && [[ "$MINOR_VERSION" -ge "11" ]]; then
+    return 0
+  else
+    return 1
+  fi
+}
diff --git a/tests/unit/git_1.bats b/tests/unit/git_1.bats
index cb49ea9a1..760b90f6f 100644
--- a/tests/unit/git_1.bats
+++ b/tests/unit/git_1.bats
@@ -71,3 +71,35 @@ teardown() {
   echo "status: $status"
   assert_output_exists
 }
+
+@test "(git) keep-git-dir" {
+  run /bin/bash -c "dokku git:set $TEST_APP keep-git-dir true"
+  echo "output: $output"
+  echo "status: $status"
+  assert_success
+
+  run deploy_app
+  echo "output: $output"
+  echo "status: $status"
+  assert_success
+
+  run /bin/bash -c "dokku enter $TEST_APP web ls .git"
+  echo "output: $output"
+  echo "status: $status"
+  assert_success
+  assert_output_contains "branches"
+  assert_output_contains "config"
+  assert_output_contains "description"
+  assert_output_contains "HEAD"
+  assert_output_contains "hooks"
+  assert_output_contains "index"
+  assert_output_contains "info"
+  assert_output_contains "logs"
+  assert_output_contains "objects"
+  assert_output_contains "refs"
+
+  run /bin/bash -c "dokku enter $TEST_APP web test -d .git"
+  echo "output: $output"
+  echo "status: $status"
+  assert_success
+}