diff --git a/apps/server/src/vcs/GitVcsDriverCore.test.ts b/apps/server/src/vcs/GitVcsDriverCore.test.ts
index 7802a254f127a..cc66c329ff003 100644
--- a/apps/server/src/vcs/GitVcsDriverCore.test.ts
+++ b/apps/server/src/vcs/GitVcsDriverCore.test.ts
@@ -8373,6 +8373,53 @@ it.layer(layerTest)("GitVcsDriver core integration", (it) => {
       }),
     );
 
+    it.effect("keeps other files conflicted through a selected-file commit", () =>
+      Effect.gen(function* () {
+        const cwd = yield* makeTmpDir();
+        yield* initRepoWithCommit(cwd);
+        const driver = yield* GitVcsDriver.GitVcsDriver;
+        // git stash pop leaves README.md conflicted with no merge in progress.
+        yield* writeTextFile(cwd, "README.md", "stashed version\n");
+        yield* git(cwd, ["stash"]);
+        yield* writeTextFile(cwd, "README.md", "committed version\n");
+        yield* git(cwd, ["commit", "-am", "Change README"]);
+        const pop = yield* driver.execute({
+          operation: "test.stashPop",
+          cwd,
+          args: ["stash", "pop"],
+          allowNonZeroExit: true,
+        });
+        assert.equal(pop.exitCode, 1);
+        yield* writeTextFile(cwd, "other.txt", "other\n");
+        const head = yield* git(cwd, ["rev-parse", "HEAD"]);
+        const unmerged = yield* git(cwd, ["ls-files", "--unmerged"]);
+        const fs = yield* FileSystem.FileSystem;
+        const path = yield* Path.Path;
+        const nested = path.join(cwd, "nested");
+        yield* fs.makeDirectory(nested);
+        // A formatting hook stages its edit into the temporary index that --only commits from.
+        yield* writeTextFile(
+          cwd,
+          ".git/hooks/pre-commit",
+          "#!/bin/sh\necho formatted >> other.txt\ngit add other.txt\n",
+        );
+        yield* fs.chmod(path.join(cwd, ".git/hooks/pre-commit"), 0o755);
+
+        yield* driver.commit(cwd, "Add other", "", { stage: { filePaths: ["other.txt"] } });
+
+        assert.equal(yield* git(cwd, ["rev-parse", "HEAD~1"]), head);
+        assert.equal(yield* git(cwd, ["show", "--pretty=", "--name-only", "HEAD"]), "other.txt");
+        assert.equal(yield* git(cwd, ["show", "HEAD:other.txt"]), "other\nformatted");
+        assert.equal(yield* git(cwd, ["show", ":other.txt"]), "other\nformatted");
+        assert.equal(yield* git(cwd, ["ls-files", "--unmerged"]), unmerged);
+        const all = yield* driver.prepareCommitContext(nested).pipe(Effect.flip);
+        assert.equal(
+          all.detail,
+          "Cannot commit with unresolved merge conflicts in README.md. Resolve them, then commit.",
+        );
+      }),
+    );
+
     const commitWithHooks = (hooks: Record<string, string>) =>
       Effect.gen(function* () {
         const cwd = yield* makeTmpDir();
diff --git a/apps/server/src/vcs/GitVcsDriverCore.ts b/apps/server/src/vcs/GitVcsDriverCore.ts
index 36bb3fe576cd7..316e0acb2884a 100644
--- a/apps/server/src/vcs/GitVcsDriverCore.ts
+++ b/apps/server/src/vcs/GitVcsDriverCore.ts
@@ -2679,6 +2679,7 @@ export const makeGitVcsDriverCore = Effect.fn("makeGitVcsDriverCore")(function*
     const config = env
       ? ["-c", "core.splitIndex=false", "-c", "splitIndex.sharedIndexExpire=never"]
       : [];
+    let preserveUnselectedConflicts = false;
     if (filePaths && filePaths.length > 0) {
       if (env) {
         const head = yield* executeGit(
@@ -2755,7 +2756,20 @@ export const makeGitVcsDriverCore = Effect.fn("makeGitVcsDriverCore")(function*
             detail: `Cannot commit selected files during a ${operation}. Commit all files to finish the ${operation}.`,
           });
         }
-        yield* runGit("GitVcsDriver.commit.reset", cwd, ["reset", "--quiet"]);
+        const selectedFiles = new Set(filePaths);
+        const unmergedPaths = yield* runGitStdoutWithOptions(
+          "GitVcsDriver.commit.unmergedPaths",
+          cwd,
+          ["-c", "diff.relative=false", "diff", "--cached", "--name-only", "--diff-filter=U", "-z"],
+          { maxOutputBytes: REVIEW_METADATA_MAX_OUTPUT_BYTES },
+        );
+        // Reset drops every conflict stage, so keep the index while unselected files are conflicted.
+        preserveUnselectedConflicts = unmergedPaths
+          .split("\0")
+          .some((file) => file.length > 0 && !selectedFiles.has(file));
+        if (!preserveUnselectedConflicts) {
+          yield* runGit("GitVcsDriver.commit.reset", cwd, ["reset", "--quiet"]);
+        }
       }
       // Status paths are repository-relative, while cwd can be a subdirectory.
       const pathspecs = filePaths.map((file) => `:(top,literal)${file}`);
@@ -2871,6 +2885,9 @@ export const makeGitVcsDriverCore = Effect.fn("makeGitVcsDriverCore")(function*
         env ? { env } : {},
       );
     }
+    return preserveUnselectedConflicts && filePaths
+      ? filePaths.map((file) => `:(top,literal)${file}`)
+      : undefined;
   });
 
   const prepareCommitContext: GitVcsDriver.GitVcsDriver["Service"]["prepareCommitContext"] =
@@ -3015,14 +3032,26 @@ export const makeGitVcsDriverCore = Effect.fn("makeGitVcsDriverCore")(function*
     body,
     options?: GitVcsDriver.GitCommitOptions,
   ) {
-    if (options?.stage !== undefined) {
-      yield* stageCommitChanges(cwd, options.stage.filePaths);
-    }
+    const partialCommitPaths =
+      options?.stage !== undefined
+        ? yield* stageCommitChanges(cwd, options.stage.filePaths)
+        : undefined;
     const args = ["commit", "-m", subject];
     const trimmedBody = body.trim();
     if (trimmedBody.length > 0) {
       args.push("-m", trimmedBody);
     }
+    const onlyFromStdin = partialCommitPaths ? yield* supportsPathspecFromFile(cwd) : false;
+    const onlyPathspecArgs = onlyFromStdin
+      ? ["--pathspec-from-file=-", "--pathspec-file-nul"]
+      : ["--", ...(partialCommitPaths ?? [])];
+    const onlyPathspecStdin =
+      partialCommitPaths && onlyFromStdin
+        ? { stdin: partialCommitPaths.map((pathspec) => `${pathspec}\0`).join("") }
+        : {};
+    if (partialCommitPaths) {
+      args.push("--only", ...onlyPathspecArgs);
+    }
     const progress =
       options?.progress?.onOutputLine === undefined
         ? options?.progress
@@ -3035,9 +3064,19 @@ export const makeGitVcsDriverCore = Effect.fn("makeGitVcsDriverCore")(function*
           };
     yield* executeGit("GitVcsDriver.commit.commit", cwd, args, {
       maxOutputBytes: REVIEW_METADATA_MAX_OUTPUT_BYTES,
+      ...onlyPathspecStdin,
       ...(options?.timeoutMs !== undefined ? { timeoutMs: options.timeoutMs } : {}),
       ...(progress ? { progress } : {}),
     }).pipe(Effect.asVoid);
+    if (partialCommitPaths) {
+      // --only runs hooks on a temporary index, so a hook's `git add` never reaches the real one.
+      yield* runGit(
+        "GitVcsDriver.commit.syncSelectedIndex",
+        cwd,
+        ["reset", "--quiet", "HEAD", ...onlyPathspecArgs],
+        onlyPathspecStdin,
+      );
+    }
     const commitSha = yield* runGitStdout("GitVcsDriver.commit.revParseHead", cwd, [
       "rev-parse",
       "HEAD",