diff --git a/dvc/api.py b/dvc/api.py
index f9b2f4fe5..b7de3682e 100644
--- a/dvc/api.py
+++ b/dvc/api.py
@@ -121,12 +121,13 @@ def make_checkpoint():
     import builtins
     from time import sleep
 
+    from dvc.env import DVC_CHECKPOINT, DVC_ROOT
     from dvc.stage.run import CHECKPOINT_SIGNAL_FILE
 
-    if os.getenv("DVC_CHECKPOINT") is None:
+    if os.getenv(DVC_CHECKPOINT) is None:
         return
 
-    root_dir = Repo.find_root()
+    root_dir = os.getenv(DVC_ROOT, Repo.find_root())
     signal_file = os.path.join(
         root_dir, Repo.DVC_DIR, "tmp", CHECKPOINT_SIGNAL_FILE
     )
diff --git a/dvc/env.py b/dvc/env.py
index 9b5ea67a8..d1b40671c 100644
--- a/dvc/env.py
+++ b/dvc/env.py
@@ -1,2 +1,4 @@
+DVC_CHECKPOINT = "DVC_CHECKPOINT"
 DVC_DAEMON = "DVC_DAEMON"
 DVC_PAGER = "DVC_PAGER"
+DVC_ROOT = "DVC_ROOT"
diff --git a/dvc/stage/run.py b/dvc/stage/run.py
index 591350b64..68abc80c8 100644
--- a/dvc/stage/run.py
+++ b/dvc/stage/run.py
@@ -5,6 +5,7 @@ import subprocess
 import threading
 from contextlib import contextmanager
 
+from dvc.env import DVC_CHECKPOINT, DVC_ROOT
 from dvc.utils import fix_env
 
 from .decorators import relock_repo, unlocked_repo
@@ -47,7 +48,7 @@ def cmd_run(stage, *args, checkpoint_func=None, **kwargs):
     kwargs = {"cwd": stage.wdir, "env": fix_env(None), "close_fds": True}
     if checkpoint_func:
         # indicate that checkpoint cmd is being run inside DVC
-        kwargs["env"].update({"DVC_CHECKPOINT": "1"})
+        kwargs["env"].update(_checkpoint_env(stage))
 
     if os.name == "nt":
         kwargs["shell"] = True
@@ -118,6 +119,10 @@ def run_stage(stage, dry=False, force=False, checkpoint_func=None, **kwargs):
         cmd_run(stage, checkpoint_func=checkpoint_func)
 
 
+def _checkpoint_env(stage):
+    return {DVC_CHECKPOINT: "1", DVC_ROOT: stage.repo.root_dir}
+
+
 @contextmanager
 def checkpoint_monitor(stage, callback_func, proc, killed):
     if not callback_func:
diff --git a/tests/func/experiments/test_checkpoints.py b/tests/func/experiments/test_checkpoints.py
index 3d1c2d33c..503fcdac1 100644
--- a/tests/func/experiments/test_checkpoints.py
+++ b/tests/func/experiments/test_checkpoints.py
@@ -4,6 +4,7 @@ from textwrap import dedent
 import pytest
 from funcy import first
 
+import dvc as dvc_module
 from dvc.exceptions import DvcException
 from dvc.repo.experiments import Experiments
 
@@ -62,10 +63,15 @@ def checkpoint_stage(tmp_dir, scm, dvc):
 
 
 def test_new_checkpoint(tmp_dir, scm, dvc, checkpoint_stage, mocker):
+    from dvc.env import DVC_CHECKPOINT, DVC_ROOT
+
     new_mock = mocker.spy(dvc.experiments, "new")
+    env_mock = mocker.spy(dvc_module.stage.run, "_checkpoint_env")
     dvc.experiments.run(checkpoint_stage.addressing, params=["foo=2"])
 
     new_mock.assert_called_once()
+    env_mock.assert_called_once()
+    assert set(env_mock.return_value.keys()) == {DVC_CHECKPOINT, DVC_ROOT}
     assert (tmp_dir / "foo").read_text() == "5"
     assert (
         tmp_dir / ".dvc" / "experiments" / "metrics.yaml"