diff --git a/detect_secrets_server/actions/initialize.py b/detect_secrets_server/actions/initialize.py
index 4f18597..0b33f43 100644
--- a/detect_secrets_server/actions/initialize.py
+++ b/detect_secrets_server/actions/initialize.py
@@ -127,6 +127,7 @@ def _clone_and_save_repo(repo):
     # Make the last_commit_hash of repo point to HEAD
     if not repo.last_commit_hash:
         repo.update()
+        return repo.save(OverrideLevel.ALWAYS)
 
     # Save the last_commit_hash, if we have nothing on file already
     return repo.save(OverrideLevel.NEVER)
diff --git a/detect_secrets_server/actions/scan.py b/detect_secrets_server/actions/scan.py
index d3a7a7e..0307296 100644
--- a/detect_secrets_server/actions/scan.py
+++ b/detect_secrets_server/actions/scan.py
@@ -2,6 +2,7 @@
 
 from detect_secrets.core.log import log
 
+from detect_secrets_server.actions.initialize import _clone_and_save_repo
 from detect_secrets_server.repos.base_tracked_repo import OverrideLevel
 from detect_secrets_server.repos.factory import tracked_repo_factory
 
@@ -26,6 +27,10 @@ def scan_repo(args):
         log.error('Unable to find repo: %s', args.repo)
         return 1
 
+    # if last_commit_hash is empty, re-clone and see if there's an initial commit hash
+    if repo.last_commit_hash is None:
+        _clone_and_save_repo(repo)
+
     secrets = repo.scan(
         exclude_files_regex=args.exclude_files,
         exclude_lines_regex=args.exclude_lines,
diff --git a/detect_secrets_server/storage/core/git.py b/detect_secrets_server/storage/core/git.py
index 667b859..e2f68f8 100644
--- a/detect_secrets_server/storage/core/git.py
+++ b/detect_secrets_server/storage/core/git.py
@@ -4,6 +4,9 @@
 import os
 import re
 import subprocess
+import sys
+
+from detect_secrets.core.log import log
 
 from detect_secrets_server.constants import IGNORED_FILE_EXTENSIONS
 
@@ -175,16 +178,39 @@ def _filter_filenames_from_diff(directory, last_commit_hash):
 
 
 def _git(directory, *args, **kwargs):
-    output = subprocess.check_output(
-        [
-            'git',
-            '--git-dir', directory,
-        ] + list(args),
-        stderr=subprocess.STDOUT
-    ).decode('utf-8', errors='ignore')
-
-    # This is to fix https://github.com/matiasb/python-unidiff/issues/54
-    if not kwargs.get('should_strip_output', True):
-        return output
-
-    return output.strip()
+    try:
+        output = subprocess.check_output(
+            [
+                'git',
+                '--git-dir', directory,
+            ] + list(args),
+            stderr=subprocess.STDOUT
+        ).decode('utf-8', errors='ignore')
+
+        # This is to fix https://github.com/matiasb/python-unidiff/issues/54
+        if not kwargs.get('should_strip_output', True):
+            return output
+        return output.strip()
+    except subprocess.CalledProcessError as e:
+        error_message = e.output.decode('utf-8')
+
+        # Catch this error, this happens during scanning and means it's an empty repo. This bails out
+        # of the scan process and logs error.
+        if re.match(
+            r"fatal: couldn't find remote ref (None|HEAD)",
+            error_message
+        ):
+            # directory is the best/only output without drastic rewrites, hashed path correlates to repo
+            log.error("Empty repository cannot be scanned: %s", directory)
+            sys.exit(1)
+            # TODO: This won't work if scan loops through repos, but works since it's a single scan currently
+
+        # Catch this error, this happens during initialization and means it's an empty repo. This allows
+        # the repo metadata to be written to /tracked
+        elif re.match(
+                r"fatal: ambiguous argument 'HEAD': unknown revision or path not in the working tree.",
+                error_message
+        ):
+            return None
+        else:
+            raise
diff --git a/tests/actions/initialize_test.py b/tests/actions/initialize_test.py
index f2c7ede..73e0755 100644
--- a/tests/actions/initialize_test.py
+++ b/tests/actions/initialize_test.py
@@ -224,7 +224,7 @@ def test_add_non_local_repo(self, mock_file_operations, mock_rootdir):
             ),
         )
 
-    def test_never_override_meta_tracking_if_already_exists(
+    def test_override_meta_tracking_if_already_exists(
         self,
         mock_file_operations,
         mock_rootdir,
@@ -237,7 +237,7 @@ def test_never_override_meta_tracking_if_already_exists(
         ):
             self.add_non_local_repo(mock_rootdir)
 
-        assert not mock_file_operations.write.called
+        assert mock_file_operations.write.called
 
     def add_non_local_repo(self, mock_rootdir):
         repo = 'git@github.com:yelp/detect-secrets'