diff --git a/src/components/ProjectSettingsModal.tsx b/src/components/ProjectSettingsModal.tsx
index 80f97923..24cfbf25 100644
--- a/src/components/ProjectSettingsModal.tsx
+++ b/src/components/ProjectSettingsModal.tsx
@@ -204,6 +204,13 @@ export function ProjectSettingsModal({
   const [settings, setSettings] = useState<ProjectSettings>(() =>
     defaultProjectSettings(),
   );
+  const [settingsByRoot, setSettingsByRoot] = useState<
+    Record<string, ProjectSettings>
+  >({});
+  const [dirtyWorktreeRoots, setDirtyWorktreeRoots] = useState<Set<string>>(
+    () => new Set(),
+  );
+  const [worktreeRootPath, setWorktreeRootPath] = useState("");
   const [identity, setIdentity] = useState<string | null>(null);
   const [worktrees, setWorktrees] = useState<RootedWorktree[]>([]);
   const [branches, setBranches] = useState<ProjectBranch[]>([]);
@@ -269,9 +276,25 @@ export function ProjectSettingsModal({
     setName(projectName);
   }, [project?.repoPath, projectName]);
 
+  useEffect(() => {
+    const requestedRoot = project?.repoPath;
+    setWorktreeRootPath(
+      requestedRoot && projectRoots.includes(requestedRoot)
+        ? requestedRoot
+        : (projectRoots[0] ?? ""),
+    );
+  }, [project?.repoPath, projectRootsKey]);
+
+  const activeWorktreeRoot = projectRoots.includes(worktreeRootPath)
+    ? worktreeRootPath
+    : (projectRoots[0] ?? "");
+
   useEffect(() => {
     if (!project) {
       setSettings(defaultProjectSettings());
+      setSettingsByRoot({});
+      setDirtyWorktreeRoots(new Set());
+      setWorktreeRootPath("");
       setIdentity(null);
       setWorktrees([]);
       setBranches([]);
@@ -290,24 +313,36 @@ export function ProjectSettingsModal({
     let cancelled = false;
     setLoading(true);
     setWorktreesLoading(true);
-    setBranchesLoading(true);
-    setBranches([]);
     setRemovingPath(null);
     setConfirmRemove(null);
     setError(null);
     setWorktreeError(null);
     setBranchError(null);
 
-    api
-      .getProjectSettings(project.repoPath)
-      .then((record) => {
+    Promise.all(
+      projectRoots.map(async (rootPath) => ({
+        rootPath,
+        record: await api.getProjectSettings(rootPath),
+      })),
+    )
+      .then((entries) => {
         if (cancelled) return;
-        setSettings(record.settings);
-        setIdentity(record.key);
+        const nextByRoot = Object.fromEntries(
+          entries.map(({ rootPath, record }) => [rootPath, record.settings]),
+        );
+        const currentRecord = entries.find(
+          ({ rootPath }) => rootPath === project.repoPath,
+        )?.record;
+        setSettings(currentRecord?.settings ?? defaultProjectSettings());
+        setSettingsByRoot(nextByRoot);
+        setDirtyWorktreeRoots(new Set());
+        setIdentity(currentRecord?.key ?? null);
       })
       .catch((e) => {
         if (cancelled) return;
         setSettings(defaultProjectSettings());
+        setSettingsByRoot({});
+        setDirtyWorktreeRoots(new Set());
         setIdentity(null);
         setError(String(e));
       })
@@ -329,11 +364,28 @@ export function ProjectSettingsModal({
         if (!cancelled) setWorktreesLoading(false);
       });
 
+    return () => {
+      cancelled = true;
+    };
+    // eslint-disable-next-line react-hooks/exhaustive-deps
+  }, [project, projectRootsKey]);
+
+  useEffect(() => {
+    if (!project || !activeWorktreeRoot) {
+      setBranches([]);
+      setBranchesLoading(false);
+      setBranchError(null);
+      return;
+    }
+
+    let cancelled = false;
+    setBranches([]);
+    setBranchesLoading(true);
+    setBranchError(null);
     api
-      .listProjectBranches(project.repoPath)
+      .listProjectBranches(activeWorktreeRoot)
       .then((items) => {
-        if (cancelled) return;
-        setBranches(items);
+        if (!cancelled) setBranches(items);
       })
       .catch((e) => {
         if (cancelled) return;
@@ -347,11 +399,15 @@ export function ProjectSettingsModal({
     return () => {
       cancelled = true;
     };
-    // eslint-disable-next-line react-hooks/exhaustive-deps
-  }, [project, projectRootsKey]);
+  }, [project, activeWorktreeRoot]);
 
   const prompt = settings.pull_requests.generation_prompt ?? "";
-  const configuredBaseBranch = settings.worktrees.base_branch;
+  const activeRootSettings =
+    settingsByRoot[activeWorktreeRoot] ??
+    (activeWorktreeRoot === project?.repoPath
+      ? settings
+      : defaultProjectSettings());
+  const configuredBaseBranch = activeRootSettings.worktrees.base_branch;
   const configuredProjectBranch = branches.find(
     (branch) => projectBranchReference(branch) === configuredBaseBranch,
   ) ?? branches.find((branch) => branch.name === configuredBaseBranch);
@@ -401,6 +457,11 @@ export function ProjectSettingsModal({
       },
     ];
   }, [branches, t]);
+  const worktreeRootOptions: SelectItem[] = projectRoots.map((rootPath) => ({
+    value: rootPath,
+    label: rootPath,
+    searchText: `${basenamePath(rootPath)} ${rootPath}`,
+  }));
 
   function updatePrompt(value: string) {
     const next = Array.from(value).slice(0, PROMPT_MAX_CHARS).join("");
@@ -420,31 +481,44 @@ export function ProjectSettingsModal({
     }));
   }
 
-  function updateWorktreeBaseBranch(value: string) {
-    const next = Array.from(value).slice(0, BRANCH_MAX_CHARS).join("");
-    setSettings((current) => ({
-      ...current,
-      worktrees: {
-        ...current.worktrees,
-        base_branch: next,
-      },
-    }));
+  function updateWorktreeBaseBranch(value: string | null) {
+    if (!activeWorktreeRoot) return;
+    const next =
+      value === null
+        ? null
+        : Array.from(value).slice(0, BRANCH_MAX_CHARS).join("");
+    setSettingsByRoot((current) => {
+      const currentSettings =
+        current[activeWorktreeRoot] ??
+        (activeWorktreeRoot === project?.repoPath
+          ? settings
+          : defaultProjectSettings());
+      return {
+        ...current,
+        [activeWorktreeRoot]: {
+          ...currentSettings,
+          worktrees: {
+            ...currentSettings.worktrees,
+            base_branch: next,
+          },
+        },
+      };
+    });
+    setDirtyWorktreeRoots((current) => {
+      const nextRoots = new Set(current);
+      nextRoots.add(activeWorktreeRoot);
+      return nextRoots;
+    });
   }
 
   function selectWorktreeBaseBranch(value: string) {
     if (value === AUTOMATIC_BASE_BRANCH_VALUE) {
-      setSettings((current) => ({
-        ...current,
-        worktrees: { ...current.worktrees, base_branch: null },
-      }));
+      updateWorktreeBaseBranch(null);
       return;
     }
     if (value === CUSTOM_BASE_BRANCH_VALUE) {
       if (selectedBaseBranch !== CUSTOM_BASE_BRANCH_VALUE) {
-        setSettings((current) => ({
-          ...current,
-          worktrees: { ...current.worktrees, base_branch: "" },
-        }));
+        updateWorktreeBaseBranch("");
       }
       return;
     }
@@ -472,9 +546,18 @@ export function ProjectSettingsModal({
           return;
         }
       }
+      for (const rootPath of dirtyWorktreeRoots) {
+        if (rootPath === project.repoPath) continue;
+        const rootSettings = settingsByRoot[rootPath];
+        if (rootSettings) {
+          await api.updateProjectSettings(rootPath, rootSettings);
+        }
+      }
+      const currentRootWorktreeSettings =
+        settingsByRoot[project.repoPath]?.worktrees ?? settings.worktrees;
       const record = await api.updateProjectSettings(
         project.repoPath,
-        settings,
+        { ...settings, worktrees: currentRootWorktreeSettings },
       );
       setSettings(record.settings);
       setIdentity(record.key);
@@ -655,6 +738,34 @@ export function ProjectSettingsModal({
                   title={dt(t, "dialogs.projectSettings.worktrees")}
                   description={dt(t, "dialogs.projectSettings.worktreesHint")}
                 >
+                  {projectRoots.length > 1 ? (
+                    <Field
+                      label={dt(
+                        t,
+                        "dialogs.projectSettings.worktreeRepository",
+                      )}
+                      hint={dt(
+                        t,
+                        "dialogs.projectSettings.worktreeRepositoryHint",
+                      )}
+                    >
+                      <Select
+                        value={activeWorktreeRoot}
+                        onValueChange={setWorktreeRootPath}
+                        options={worktreeRootOptions}
+                        searchable
+                        disabled={loading || saving}
+                        aria-label={dt(
+                          t,
+                          "dialogs.projectSettings.worktreeRepository",
+                        )}
+                        searchPlaceholder={dt(
+                          t,
+                          "dialogs.projectSettings.searchRepositories",
+                        )}
+                      />
+                    </Field>
+                  ) : null}
                   <Field
                     label={dt(t, "dialogs.projectSettings.worktreeBaseBranch")}
                     hint={dt(
diff --git a/src/locales/en.json b/src/locales/en.json
index c5dc66ca..77e39d90 100644
--- a/src/locales/en.json
+++ b/src/locales/en.json
@@ -2198,6 +2198,9 @@
       "pullRequestsHint": "Project-specific defaults for pull request workflows.",
       "worktrees": "Worktrees",
       "worktreesHint": "Defaults and linked git worktrees for this project.",
+      "worktreeRepository": "Repository for new worktrees",
+      "worktreeRepositoryHint": "Each repository root keeps its own base branch setting.",
+      "searchRepositories": "Search repositories",
       "worktreeBaseBranch": "Base branch for new worktrees",
       "worktreeBaseBranchHint": "Choose a local or remote-tracking branch, or enter another branch name. Automatic chooses main, master, or the current HEAD.",
       "worktreeBaseBranchAutomatic": "Automatic",
diff --git a/src/locales/ja.json b/src/locales/ja.json
index 664eb01c..11dc95b0 100644
--- a/src/locales/ja.json
+++ b/src/locales/ja.json
@@ -2198,6 +2198,9 @@
       "pullRequestsHint": "プル リクエスト ワークフローのプロジェクト固有のデフォルト。",
       "worktrees": "ワークツリー",
       "worktreesHint": "このプロジェクトの既定値とリンクされた Git ワークツリー。",
+      "worktreeRepository": "新しいワークツリーのリポジトリ",
+      "worktreeRepositoryHint": "リポジトリルートごとに独自のベースブランチ設定を保持します。",
+      "searchRepositories": "リポジトリを検索",
       "worktreeBaseBranch": "新しいワークツリーのベースブランチ",
       "worktreeBaseBranchHint": "ローカルまたはリモート追跡ブランチを選択するか、別のブランチ名を入力します。自動選択では main、master、または現在の HEAD を使用します。",
       "worktreeBaseBranchAutomatic": "自動選択",
diff --git a/src/locales/ko.json b/src/locales/ko.json
index e96177b1..94bd762e 100644
--- a/src/locales/ko.json
+++ b/src/locales/ko.json
@@ -2198,6 +2198,9 @@
       "pullRequestsHint": "이 프로젝트의 pull request 작업에만 적용되는 기본값입니다.",
       "worktrees": "워크트리",
       "worktreesHint": "이 프로젝트의 기본값과 연결 Git 워크트리입니다.",
+      "worktreeRepository": "새 워크트리를 만들 저장소",
+      "worktreeRepositoryHint": "각 저장소 루트는 자체 기준 브랜치 설정을 사용합니다.",
+      "searchRepositories": "저장소 검색",
       "worktreeBaseBranch": "새 워크트리의 기준 브랜치",
       "worktreeBaseBranchHint": "로컬 또는 원격 추적 브랜치를 선택하거나 다른 브랜치 이름을 직접 입력하세요. 자동 선택은 main, master 또는 현재 HEAD를 사용합니다.",
       "worktreeBaseBranchAutomatic": "자동 선택",
diff --git a/src/locales/zh-CN.json b/src/locales/zh-CN.json
index 3c5c01cd..762b8a56 100644
--- a/src/locales/zh-CN.json
+++ b/src/locales/zh-CN.json
@@ -2198,6 +2198,9 @@
       "pullRequestsHint": "项目特定的默认值为拉取请求工作流。",
       "worktrees": "工作树",
       "worktreesHint": "此项目的默认值和已注册的链接 Git 工作树。",
+      "worktreeRepository": "新工作树的仓库",
+      "worktreeRepositoryHint": "每个仓库根目录保留自己的基准分支设置。",
+      "searchRepositories": "搜索仓库",
       "worktreeBaseBranch": "新工作树的基准分支",
       "worktreeBaseBranchHint": "选择本地或远程跟踪分支，或输入其他分支名称。自动选择将使用 main、master 或当前 HEAD。",
       "worktreeBaseBranchAutomatic": "自动选择",
diff --git a/tests/e2e/project-settings.spec.ts b/tests/e2e/project-settings.spec.ts
index ed36e953..4ce6c423 100644
--- a/tests/e2e/project-settings.spec.ts
+++ b/tests/e2e/project-settings.spec.ts
@@ -289,6 +289,123 @@ test.describe("project settings", () => {
     ]);
   });
 
+  test("saves a separate base branch for each project source root", async ({
+    page,
+    tauri,
+  }) => {
+    await tauri.respond("list_projects", [
+      {
+        repo_path: "/tmp/acorn",
+        name: "acorn",
+        created_at: "2026-01-01T00:00:00Z",
+        position: 0,
+        source_paths: ["/tmp/backoffice"],
+      },
+    ]);
+    await tauri.handle("get_project_settings", (args) => {
+      const repoPath = (args as { repoPath: string }).repoPath;
+      const source = repoPath === "/tmp/backoffice";
+      return {
+        key: `path:${repoPath}`,
+        settings: {
+          remember_after_close: !source,
+          pull_requests: {
+            generation_prompt: source ? "Backoffice prompt" : "Acorn prompt",
+          },
+          worktrees: {
+            base_branch: source
+              ? "refs/heads/release/backoffice"
+              : "refs/heads/develop",
+          },
+        },
+      };
+    });
+    await tauri.handle("list_project_branches", (args) => {
+      const w = window as unknown as { __branchRootCalls?: string[] };
+      const repoPath = (args as { repoPath: string }).repoPath;
+      w.__branchRootCalls = [...(w.__branchRootCalls ?? []), repoPath];
+      return repoPath === "/tmp/backoffice"
+        ? [
+            { name: "main", is_remote: false },
+            { name: "release/backoffice", is_remote: false },
+          ]
+        : [
+            { name: "main", is_remote: false },
+            { name: "develop", is_remote: false },
+          ];
+    });
+    await tauri.handle("update_project_settings", (args) => {
+      const w = window as unknown as { __settingsRootCalls?: unknown[] };
+      w.__settingsRootCalls = [...(w.__settingsRootCalls ?? []), args];
+      const input = args as {
+        repoPath: string;
+        settings: Record<string, unknown>;
+      };
+      return { key: `path:${input.repoPath}`, settings: input.settings };
+    });
+
+    await page.goto("/");
+    await page
+      .getByRole("button", { name: "Project acorn" })
+      .click({ button: "right" });
+    await page.getByRole("menuitem", { name: "Project Settings" }).click();
+
+    const modal = page.getByRole("dialog", { name: "Project Settings" });
+    await modal.getByRole("button", { name: "Worktrees" }).click();
+    const repository = modal.getByRole("combobox", {
+      name: "Repository for new worktrees",
+    });
+    await expect(repository).toContainText("/tmp/acorn");
+    await repository.click();
+    await page.getByRole("option", { name: /backoffice/ }).click();
+
+    const baseBranch = modal.getByRole("combobox", {
+      name: "Base branch for new worktrees",
+    });
+    await expect(baseBranch).toContainText("release/backoffice");
+    await baseBranch.click();
+    await page.getByRole("option", { name: "main", exact: true }).click();
+    await modal.getByRole("button", { name: "Save" }).click();
+
+    const calls = (await page.evaluate(
+      () =>
+        (window as unknown as { __settingsRootCalls?: unknown[] })
+          .__settingsRootCalls,
+    )) as Array<{
+      repoPath: string;
+      settings: {
+        remember_after_close: boolean;
+        pull_requests: { generation_prompt: string };
+        worktrees: { base_branch: string };
+      };
+    }>;
+    expect(calls).toEqual([
+      {
+        repoPath: "/tmp/backoffice",
+        settings: {
+          remember_after_close: false,
+          pull_requests: { generation_prompt: "Backoffice prompt" },
+          worktrees: { base_branch: "refs/heads/main" },
+        },
+      },
+      {
+        repoPath: "/tmp/acorn",
+        settings: {
+          remember_after_close: true,
+          pull_requests: { generation_prompt: "Acorn prompt" },
+          worktrees: { base_branch: "refs/heads/develop" },
+        },
+      },
+    ]);
+    const branchRoots = await page.evaluate(
+      () =>
+        (window as unknown as { __branchRootCalls?: string[] })
+          .__branchRootCalls ?? [],
+    );
+    expect(branchRoots).toContain("/tmp/acorn");
+    expect(branchRoots).toContain("/tmp/backoffice");
+  });
+
   test("accepts a base branch name that is not in the detected list", async ({
     page,
     tauri,