--- a/src/aerie/sync.py
+++ b/src/aerie/sync.py
@@ -54,6 +54,10 @@ def clone_repo(repo: RepoConfig, release: str) -> None:
     run(["git", "clone", "--branch", release, repo.sync_uri, str(repo.location)])
 
 
+def is_empty_dir(path: Path) -> bool:
+    return path.is_dir() and not any(path.iterdir())
+
+
 def update_repo(repo: RepoConfig, release: str) -> None:
     ensure_clean_git_tree(repo.location)
     run(["git", "-C", str(repo.location), "fetch", "--prune", "origin"])
@@ -70,6 +74,9 @@ def sync_repo(repo: RepoConfig, release: str) -> None:
         clone_repo(repo, release)
         return
     if not (repo.location / ".git").exists():
+        if is_empty_dir(repo.location):
+            clone_repo(repo, release)
+            return
         raise AerieError(f"{repo.location} exists but is not a git repository")
     update_repo(repo, release)
 
--- /dev/null
+++ b/tests/test_sync.py
@@ -0,0 +1,95 @@
+from contextlib import redirect_stdout
+from io import StringIO
+from pathlib import Path
+from tempfile import TemporaryDirectory
+import unittest
+from unittest.mock import patch
+
+from aerie.config import AerieError, ProgramConfig, RepoConfig
+from aerie.sync import sync_all, sync_repo
+
+
+def repo_config(location: Path) -> RepoConfig:
+    return RepoConfig(
+        name="srcux",
+        main_repo="srcux",
+        location=location,
+        auto_sync=True,
+        sync_type="git",
+        sync_uri="https://example.test/repo.git",
+        priority="1",
+    )
+
+
+class SyncTests(unittest.TestCase):
+    def test_sync_repo_clones_into_empty_existing_directory(self):
+        with TemporaryDirectory() as tmp:
+            location = Path(tmp) / "baldeagleos"
+            location.mkdir()
+            repo = repo_config(location)
+
+            with redirect_stdout(StringIO()), patch("aerie.sync.run") as run:
+                sync_repo(repo, "develop")
+
+        run.assert_called_once_with(
+            [
+                "git",
+                "clone",
+                "--branch",
+                "develop",
+                "https://example.test/repo.git",
+                str(location),
+            ]
+        )
+
+    def test_sync_repo_rejects_non_empty_non_git_directory(self):
+        with TemporaryDirectory() as tmp:
+            location = Path(tmp) / "baldeagleos"
+            location.mkdir()
+            (location / "README").write_text("not a git checkout\n", encoding="utf-8")
+            repo = repo_config(location)
+
+            with redirect_stdout(StringIO()), patch("aerie.sync.run") as run:
+                with self.assertRaisesRegex(AerieError, "exists but is not a git repository"):
+                    sync_repo(repo, "develop")
+
+        run.assert_not_called()
+
+    def test_sync_all_clones_repo_location_created_by_path_check(self):
+        with TemporaryDirectory() as tmp:
+            tmp_path = Path(tmp)
+            location = tmp_path / "repos" / "baldeagleos"
+            repos_conf = tmp_path / "baldeagleos.conf"
+            repos_conf.write_text(
+                f"""
+[DEFAULT]
+main-repo = srcux
+
+[srcux]
+location = {location}
+auto-sync = yes
+sync-type = git
+sync-uri = https://example.test/repo.git
+priority = 1
+""",
+                encoding="utf-8",
+            )
+            config = ProgramConfig(release="develop", reposconfpath=repos_conf)
+
+            with redirect_stdout(StringIO()), patch("aerie.sync.run") as run:
+                sync_all(config)
+
+        run.assert_called_once_with(
+            [
+                "git",
+                "clone",
+                "--branch",
+                "develop",
+                "https://example.test/repo.git",
+                str(location),
+            ]
+        )
+
+
+if __name__ == "__main__":
+    unittest.main()