diff --git a/packages/server/src/utils/checkout-git.patch-format.test.ts b/packages/server/src/utils/checkout-git.patch-format.test.ts
index 834a41b871..d30ae1d7ce 100644
--- a/packages/server/src/utils/checkout-git.patch-format.test.ts
+++ b/packages/server/src/utils/checkout-git.patch-format.test.ts
@@ -1,13 +1,14 @@
 import { execFileSync } from "node:child_process";
-import { mkdirSync, mkdtempSync, realpathSync, rmSync, writeFileSync } from "node:fs";
+import { existsSync, mkdirSync, mkdtempSync, realpathSync, rmSync, writeFileSync } from "node:fs";
 import { tmpdir } from "node:os";
 import { join } from "node:path";
-import { afterEach, describe, expect, it } from "vitest";
+import { afterEach, describe, expect, it, vi } from "vitest";
 import { getCheckoutDiff, getCommitFileDiff } from "./checkout-git.js";
 
 const repos: string[] = [];
 
 afterEach(() => {
+  vi.unstubAllEnvs();
   for (const repo of repos.splice(0)) rmSync(repo, { recursive: true, force: true });
 });
 
@@ -62,6 +63,95 @@ function createChangedRepo(config: string): string {
   return cwd;
 }
 
+function createExternalDiffCommand() {
+  const directory = realpathSync.native(mkdtempSync(join(tmpdir(), "checkout-external-diff-")));
+  repos.push(directory);
+  const script = join(directory, "external-diff.cjs");
+  const marker = join(directory, "invoked");
+  writeFileSync(
+    script,
+    'require("node:fs").writeFileSync(process.argv[2], "invoked");\n' +
+      'process.stdout.write("CUSTOM EXTERNAL DIFF\\n");\n',
+  );
+  const command = [process.execPath, script, marker]
+    .map((argument) => `'${argument.replaceAll("'", "'\\''")}'`)
+    .join(" ");
+  return { command, marker };
+}
+
+function createExternalDiffRepo() {
+  vi.stubEnv("GIT_EXTERNAL_DIFF", undefined);
+  const cwd = createChangedRepo("color.diff=always");
+  const { command, marker } = createExternalDiffCommand();
+  git(cwd, "config", "diff.external", command);
+  expect(git(cwd, "diff", "HEAD", "--", "file.txt")).toBe("CUSTOM EXTERNAL DIFF\n");
+  expect(existsSync(marker)).toBe(true);
+  rmSync(marker);
+  return { cwd, command, marker };
+}
+
+function expectStandardPatch(result: Awaited<ReturnType<typeof getCheckoutDiff>>) {
+  expect(result.structured).toMatchObject([
+    {
+      path: "file.txt",
+      additions: 1,
+      deletions: 1,
+      status: "ok",
+      hunks: [
+        {
+          lines: [
+            { type: "header", content: "@@ -1 +1 @@" },
+            { type: "remove", content: "before" },
+            { type: "add", content: "after" },
+          ],
+        },
+      ],
+    },
+  ]);
+}
+
+it("returns Git patch hunks when a repository configures an external diff command", async () => {
+  const { cwd, command, marker } = createExternalDiffRepo();
+
+  const result = await getCheckoutDiff(cwd, { mode: "uncommitted", includeStructured: true });
+
+  expectStandardPatch(result);
+  expect(existsSync(marker)).toBe(false);
+  expect(git(cwd, "config", "--get", "diff.external").trim()).toBe(command);
+});
+
+it("returns Git patch hunks against the base branch with an external diff command", async () => {
+  const { cwd, command, marker } = createExternalDiffRepo();
+  git(cwd, "checkout", "-b", "feature");
+  git(cwd, "add", ".");
+  git(cwd, "-c", "commit.gpgsign=false", "commit", "-m", "edit");
+
+  const result = await getCheckoutDiff(cwd, {
+    mode: "base",
+    baseRef: "main",
+    includeStructured: true,
+  });
+
+  expectStandardPatch(result);
+  expect(existsSync(marker)).toBe(false);
+  expect(git(cwd, "config", "--get", "diff.external").trim()).toBe(command);
+});
+
+it("returns Git patch hunks when GIT_EXTERNAL_DIFF configures the external command", async () => {
+  const cwd = createChangedRepo("color.diff=always");
+  const { command, marker } = createExternalDiffCommand();
+  vi.stubEnv("GIT_EXTERNAL_DIFF", command);
+  expect(git(cwd, "diff", "HEAD", "--", "file.txt")).toBe("CUSTOM EXTERNAL DIFF\n");
+  expect(existsSync(marker)).toBe(true);
+  rmSync(marker);
+
+  const result = await getCheckoutDiff(cwd, { mode: "uncommitted", includeStructured: true });
+
+  expectStandardPatch(result);
+  expect(existsSync(marker)).toBe(false);
+  expect(process.env.GIT_EXTERNAL_DIFF).toBe(command);
+});
+
 describe.each(["diff.mnemonicPrefix=true", "color.diff=always"])(
   "patch format with %s",
   (config) => {
diff --git a/packages/server/src/utils/checkout-git.test.ts b/packages/server/src/utils/checkout-git.test.ts
index 47d2aa76ea..21791fa49e 100644
--- a/packages/server/src/utils/checkout-git.test.ts
+++ b/packages/server/src/utils/checkout-git.test.ts
@@ -1627,9 +1627,11 @@ const x = 1;
     expect(diff.diff).toContain("# generated.js: diff too large omitted");
     expect(diff.diff).toContain(`-export const value = "old";`);
     expect(diff.diff).toContain(`+export const value = "new";`);
-    expect(commands).toContain("diff --no-color --src-prefix=a/ --dst-prefix=b/ --numstat HEAD");
     expect(commands).toContain(
-      "diff --no-color --src-prefix=a/ --dst-prefix=b/ HEAD -- :(literal)generated.js :(literal)small.ts",
+      "diff --no-ext-diff --no-color --src-prefix=a/ --dst-prefix=b/ --numstat HEAD",
+    );
+    expect(commands).toContain(
+      "diff --no-ext-diff --no-color --src-prefix=a/ --dst-prefix=b/ HEAD -- :(literal)generated.js :(literal)small.ts",
     );
     expect(metrics.maxConcurrent).toBeLessThanOrEqual(8);
   });
diff --git a/packages/server/src/utils/checkout-git.ts b/packages/server/src/utils/checkout-git.ts
index 9b31fd6665..2e317810ba 100644
--- a/packages/server/src/utils/checkout-git.ts
+++ b/packages/server/src/utils/checkout-git.ts
@@ -637,7 +637,7 @@ function normalizeNumstatPath(pathField: string): string {
 }
 
 // Parsed patches need a stable wire format regardless of terminal presentation settings.
-const GIT_PATCH_FORMAT_ARGS = ["--no-color", "--src-prefix=a/", "--dst-prefix=b/"];
+const GIT_PATCH_FORMAT_ARGS = ["--no-ext-diff", "--no-color", "--src-prefix=a/", "--dst-prefix=b/"];
 
 function buildGitDiffArgs(args: { ignoreWhitespace?: boolean; extra: string[] }): string[] {
   return [