diff --git a/pre_commit/commands/autoupdate.py b/pre_commit/commands/autoupdate.py
index 33a347302..5cb978e92 100644
--- a/pre_commit/commands/autoupdate.py
+++ b/pre_commit/commands/autoupdate.py
@@ -36,24 +36,36 @@ def from_config(cls, config: Dict[str, Any]) -> 'RevInfo':
         return cls(config['repo'], config['rev'], None)
 
     def update(self, tags_only: bool, freeze: bool) -> 'RevInfo':
+        git_cmd = ('git', *git.NO_FS_MONITOR)
+
         if tags_only:
-            tag_cmd = ('git', 'describe', 'FETCH_HEAD', '--tags', '--abbrev=0')
+            tag_cmd = (
+                *git_cmd, 'describe',
+                'FETCH_HEAD', '--tags', '--abbrev=0',
+            )
         else:
-            tag_cmd = ('git', 'describe', 'FETCH_HEAD', '--tags', '--exact')
+            tag_cmd = (
+                *git_cmd, 'describe',
+                'FETCH_HEAD', '--tags', '--exact',
+            )
 
         with tmpdir() as tmp:
             git.init_repo(tmp, self.repo)
-            cmd_output_b('git', 'fetch', 'origin', 'HEAD', '--tags', cwd=tmp)
+            cmd_output_b(
+                *git_cmd, 'fetch', 'origin', 'HEAD', '--tags',
+                cwd=tmp,
+            )
 
             try:
                 rev = cmd_output(*tag_cmd, cwd=tmp)[1].strip()
             except CalledProcessError:
-                cmd = ('git', 'rev-parse', 'FETCH_HEAD')
+                cmd = (*git_cmd, 'rev-parse', 'FETCH_HEAD')
                 rev = cmd_output(*cmd, cwd=tmp)[1].strip()
 
             frozen = None
             if freeze:
-                exact = cmd_output('git', 'rev-parse', rev, cwd=tmp)[1].strip()
+                exact_rev_cmd = (*git_cmd, 'rev-parse', rev)
+                exact = cmd_output(*exact_rev_cmd, cwd=tmp)[1].strip()
                 if exact != rev:
                     rev, frozen = exact, rev
         return self._replace(rev=rev, frozen=frozen)
diff --git a/pre_commit/git.py b/pre_commit/git.py
index 6264529d5..883723ea1 100644
--- a/pre_commit/git.py
+++ b/pre_commit/git.py
@@ -12,9 +12,11 @@
 from pre_commit.util import cmd_output
 from pre_commit.util import cmd_output_b
 
-
 logger = logging.getLogger(__name__)
 
+# see #2046
+NO_FS_MONITOR = ('-c', 'core.useBuiltinFSMonitor=false')
+
 
 def zsplit(s: str) -> List[str]:
     s = s.strip('\0')
@@ -185,10 +187,11 @@ def init_repo(path: str, remote: str) -> None:
     if os.path.isdir(remote):
         remote = os.path.abspath(remote)
 
+    git = ('git', *NO_FS_MONITOR)
     env = no_git_env()
     # avoid the user's template so that hooks do not recurse
-    cmd_output_b('git', 'init', '--template=', path, env=env)
-    cmd_output_b('git', 'remote', 'add', 'origin', remote, cwd=path, env=env)
+    cmd_output_b(*git, 'init', '--template=', path, env=env)
+    cmd_output_b(*git, 'remote', 'add', 'origin', remote, cwd=path, env=env)
 
 
 def commit(repo: str = '.') -> None:
diff --git a/tests/commands/autoupdate_test.py b/tests/commands/autoupdate_test.py
index b2bad6014..7316eb97a 100644
--- a/tests/commands/autoupdate_test.py
+++ b/tests/commands/autoupdate_test.py
@@ -5,6 +5,7 @@
 import yaml
 
 import pre_commit.constants as C
+from pre_commit import envcontext
 from pre_commit import git
 from pre_commit import util
 from pre_commit.commands.autoupdate import _check_hooks_still_exist_at_rev
@@ -176,6 +177,14 @@ def test_autoupdate_out_of_date_repo(out_of_date, tmpdir, store):
     assert cfg.read() == fmt.format(out_of_date.path, out_of_date.head_rev)
 
 
+def test_autoupdate_with_core_useBuiltinFSMonitor(out_of_date, tmpdir, store):
+    # force the setting on "globally" for git
+    home = tmpdir.join('fakehome').ensure_dir()
+    home.join('.gitconfig').write('[core]\nuseBuiltinFSMonitor = true\n')
+    with envcontext.envcontext((('HOME', str(home)),)):
+        test_autoupdate_out_of_date_repo(out_of_date, tmpdir, store)
+
+
 def test_autoupdate_pure_yaml(out_of_date, tmpdir, store):
     with mock.patch.object(util, 'Dumper', yaml.SafeDumper):
         test_autoupdate_out_of_date_repo(out_of_date, tmpdir, store)