diff --git a/presubmit_support.py b/presubmit_support.py
index c6242495fc..3e549a281a 100755
--- a/presubmit_support.py
+++ b/presubmit_support.py
@@ -1059,7 +1059,8 @@ class _GitDiffCache(_DiffCache):
                                                 files=[],
                                                 full_move=True,
                                                 branch=self._upstream,
-                                                branch_head=self._end_commit)
+                                                branch_head=self._end_commit,
+                                                allow_prefix=True)
             # Compute a single diff for all files and parse the output; with git
             # this is much faster than computing one diff for each file.
             self._diffs_by_file = _parse_unified_diff(unified_diff)
diff --git a/scm.py b/scm.py
index 1793b400f3..1df082af97 100644
--- a/scm.py
+++ b/scm.py
@@ -1020,7 +1020,8 @@ class GIT(object):
                      branch: Optional[str] = None,
                      branch_head: str = 'HEAD',
                      full_move: bool = False,
-                     files: Optional[Iterable[str]] = None) -> str:
+                     files: Optional[Iterable[str]] = None,
+                     allow_prefix: bool = False) -> str:
         """Diffs against the upstream branch or optionally another branch.
 
         full_move means that move or copy operations should completely recreate the
@@ -1034,10 +1035,18 @@ class GIT(object):
             'diff',
             '-p',
             '--no-color',
-            '--no-prefix',
             '--no-ext-diff',
-            branch + "..." + branch_head,
         ]
+
+        if allow_prefix:
+            # explicitly setting --src-prefix and --dst-prefix is necessary in the
+            # case that diff.noprefix is set in the user's git config.
+            command.extend(['--src-prefix=a/', '--dst-prefix=b/'])
+        else:
+            command.extend(['--no-prefix'])
+
+        command.append(branch + "..." + branch_head)
+
         if full_move:
             command.append('--no-renames')
         else:
diff --git a/tests/presubmit_unittest.py b/tests/presubmit_unittest.py
index 3c6584f658..c863b9edd4 100755
--- a/tests/presubmit_unittest.py
+++ b/tests/presubmit_unittest.py
@@ -419,7 +419,8 @@ class PresubmitUnittest(PresubmitTestsBase):
                                                      files=[],
                                                      full_move=True,
                                                      branch='upstream',
-                                                     branch_head='end_commit')
+                                                     branch_head='end_commit',
+                                                     allow_prefix=True)
 
 
         f_blat = os.path.normpath('boo/blat.cc')