diff --git a/packages/server/src/utils/checkout-git.patch-format.test.ts b/packages/server/src/utils/checkout-git.patch-format.test.ts
new file mode 100644
index 0000000000..834a41b871
--- /dev/null
+++ b/packages/server/src/utils/checkout-git.patch-format.test.ts
@@ -0,0 +1,123 @@
+import { execFileSync } from "node:child_process";
+import { 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 { getCheckoutDiff, getCommitFileDiff } from "./checkout-git.js";
+
+const repos: string[] = [];
+
+afterEach(() => {
+  for (const repo of repos.splice(0)) rmSync(repo, { recursive: true, force: true });
+});
+
+it.each(["diff.mnemonicPrefix=true", "color.diff=always", "diff.noprefix=true"])(
+  "preserves batched paths, spaces and literal prefix directories with %s",
+  async (config) => {
+    const cwd = createChangedRepo(config);
+    mkdirSync(join(cwd, "a"));
+    for (const name of ["a/literal.txt", "with spaces.txt"]) {
+      writeFileSync(join(cwd, name), "before\n");
+    }
+    git(cwd, "add", "a/literal.txt", "with spaces.txt");
+    git(cwd, "-c", "commit.gpgsign=false", "commit", "-m", "add files");
+    for (const name of ["a/literal.txt", "with spaces.txt"]) {
+      writeFileSync(join(cwd, name), "after\n");
+    }
+
+    const result = await getCheckoutDiff(cwd, { mode: "uncommitted", includeStructured: true });
+
+    expect(result.structured?.map((file) => file.path)).toEqual([
+      "a/literal.txt",
+      "file.txt",
+      "with spaces.txt",
+    ]);
+    for (const file of result.structured ?? []) {
+      expect(file.hunks.flatMap((hunk) => hunk.lines)).toEqual(
+        expect.arrayContaining([
+          expect.objectContaining({ type: "remove", content: "before" }),
+          expect.objectContaining({ type: "add", content: "after" }),
+        ]),
+      );
+    }
+    expect(git(cwd, "config", "--get", config.split("=")[0]).trim()).toBe(config.split("=")[1]);
+  },
+);
+
+function git(cwd: string, ...args: string[]): string {
+  return execFileSync("git", args, { cwd, encoding: "utf8" });
+}
+
+function createChangedRepo(config: string): string {
+  const cwd = realpathSync.native(mkdtempSync(join(tmpdir(), "checkout-patch-format-")));
+  repos.push(cwd);
+  git(cwd, "init", "-b", "main");
+  git(cwd, "config", "user.name", "Test");
+  git(cwd, "config", "user.email", "test@example.com");
+  writeFileSync(join(cwd, "file.txt"), "before\n");
+  git(cwd, "add", ".");
+  git(cwd, "-c", "commit.gpgsign=false", "commit", "-m", "initial");
+  git(cwd, "config", ...config.split("="));
+  writeFileSync(join(cwd, "file.txt"), "after\n");
+  return cwd;
+}
+
+describe.each(["diff.mnemonicPrefix=true", "color.diff=always"])(
+  "patch format with %s",
+  (config) => {
+    it("returns displayable uncommitted diff lines with their file counts", async () => {
+      const cwd = createChangedRepo(config);
+      const result = await getCheckoutDiff(cwd, { mode: "uncommitted", includeStructured: true });
+
+      expect(result.structured).toHaveLength(1);
+      expect(result.structured?.[0]).toMatchObject({
+        path: "file.txt",
+        additions: 1,
+        deletions: 1,
+      });
+      expect(result.structured?.[0].hunks.flatMap((hunk) => hunk.lines)).toEqual(
+        expect.arrayContaining([
+          expect.objectContaining({ type: "remove", content: "before" }),
+          expect.objectContaining({ type: "add", content: "after" }),
+        ]),
+      );
+    });
+
+    it("returns displayable committed changes against the base branch", async () => {
+      const cwd = createChangedRepo(config);
+      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,
+      });
+
+      expect(result.structured?.[0]).toMatchObject({
+        path: "file.txt",
+        additions: 1,
+        deletions: 1,
+      });
+      expect(result.structured?.[0].hunks.flatMap((hunk) => hunk.lines)).toEqual(
+        expect.arrayContaining([expect.objectContaining({ type: "add", content: "after" })]),
+      );
+    });
+
+    it("returns displayable lines when opening an individual commit file", async () => {
+      const cwd = createChangedRepo(config);
+      git(cwd, "add", ".");
+      git(cwd, "-c", "commit.gpgsign=false", "commit", "-m", "edit");
+      const file = await getCommitFileDiff({
+        cwd,
+        sha: git(cwd, "rev-parse", "HEAD").trim(),
+        path: "file.txt",
+      });
+
+      expect(file).toMatchObject({ path: "file.txt", additions: 1, deletions: 1 });
+      expect(file?.hunks.flatMap((hunk) => hunk.lines)).toEqual(
+        expect.arrayContaining([expect.objectContaining({ type: "add", content: "after" })]),
+      );
+    });
+  },
+);
diff --git a/packages/server/src/utils/checkout-git.test.ts b/packages/server/src/utils/checkout-git.test.ts
index e5cb02d46e..596332c4a7 100644
--- a/packages/server/src/utils/checkout-git.test.ts
+++ b/packages/server/src/utils/checkout-git.test.ts
@@ -1507,8 +1507,10 @@ 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 --numstat HEAD");
-    expect(commands).toContain("diff HEAD -- :(literal)generated.js :(literal)small.ts");
+    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",
+    );
     expect(metrics.maxConcurrent).toBeLessThanOrEqual(8);
   });
 
diff --git a/packages/server/src/utils/checkout-git.ts b/packages/server/src/utils/checkout-git.ts
index 758d6ecf84..f663a52a63 100644
--- a/packages/server/src/utils/checkout-git.ts
+++ b/packages/server/src/utils/checkout-git.ts
@@ -636,8 +636,16 @@ function normalizeNumstatPath(pathField: string): string {
   return pathField;
 }
 
+// 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/"];
+
 function buildGitDiffArgs(args: { ignoreWhitespace?: boolean; extra: string[] }): string[] {
-  return ["diff", ...(args.ignoreWhitespace ? ["-w"] : []), ...args.extra];
+  return [
+    "diff",
+    ...GIT_PATCH_FORMAT_ARGS,
+    ...(args.ignoreWhitespace ? ["-w"] : []),
+    ...args.extra,
+  ];
 }
 
 const TRACKED_DIFF_NUMSTAT_MAX_BYTES = 2 * 1024 * 1024; // 2MB
@@ -2635,7 +2643,7 @@ export async function getCommitFileDiff({
   path: string;
 }): Promise<ParsedDiffFile | null> {
   const { stdout } = await runGitCommand(
-    ["show", sha, "--format=", "--diff-merges=first-parent", "--", path],
+    ["show", sha, "--format=", "--diff-merges=first-parent", ...GIT_PATCH_FORMAT_ARGS, "--", path],
     {
       cwd,
       envOverlay: READ_ONLY_GIT_ENV,