diff --git a/apps/web/src/components/BranchToolbar.logic.test.ts b/apps/web/src/components/BranchToolbar.logic.test.ts
index d5b74f1cb116..478216c4b10e 100644
--- a/apps/web/src/components/BranchToolbar.logic.test.ts
+++ b/apps/web/src/components/BranchToolbar.logic.test.ts
@@ -10,6 +10,7 @@ import {
   resolveBranchToolbarPrBranch,
   resolveLocalCheckoutBranchMismatch,
   resolveLockedWorkspaceLabel,
+  resolveWorktreeBaseBranchSeed,
   sanitizeNewRefName,
   shouldIncludeBranchPickerItem,
 } from "./BranchToolbar.logic";
@@ -255,6 +256,38 @@ describe("resolveBranchSelectionTarget", () => {
   });
 });
 
+describe("resolveWorktreeBaseBranchSeed", () => {
+  const ref = (name: string, flags: { current?: boolean; isDefault?: boolean }): VcsRef => ({
+    name,
+    current: flags.current ?? false,
+    isDefault: flags.isDefault ?? false,
+    worktreePath: null,
+  });
+  const seed = (
+    refs: ReadonlyArray<VcsRef>,
+    activeThreadBranch: string | null = null,
+    activeThreadBranchListed: boolean | null = null,
+  ) => resolveWorktreeBaseBranchSeed({ activeThreadBranch, activeThreadBranchListed, refs });
+
+  it("prefers the default branch, then the current listed branch", () => {
+    expect(seed([ref("feature", { current: true }), ref("staging", { isDefault: true })])).toBe(
+      "staging",
+    );
+    expect(seed([ref("feature", { current: true })])).toBe("feature");
+  });
+
+  it("has no candidate while the repository has no refs yet, such as mid-clone", () => {
+    expect(seed([])).toBeNull();
+  });
+
+  it("replaces a base the repository does not list, such as an unborn main after a clone", () => {
+    const refs = [ref("staging", { current: true, isDefault: true })];
+    expect(seed(refs, "main", false)).toBe("staging");
+    expect(seed(refs, "main", null)).toBeNull();
+    expect(seed(refs, "feature", true)).toBeNull();
+  });
+});
+
 describe("isWorktreeChangeBlocked", () => {
   const runtime = (status: "preparing" | "running" | "completed") => ({
     status,
diff --git a/apps/web/src/components/BranchToolbar.logic.ts b/apps/web/src/components/BranchToolbar.logic.ts
index 5dec87e3d73d..0bc88de2d1b5 100644
--- a/apps/web/src/components/BranchToolbar.logic.ts
+++ b/apps/web/src/components/BranchToolbar.logic.ts
@@ -186,6 +186,19 @@ export function resolveDraftEnvModeAfterBranchChange(input: {
   return "local";
 }
 
+// Only listed refs qualify: an unborn HEAD (e.g. mid-clone) names a branch that does not exist yet.
+// A base the repository confirms it does not list, such as that unborn HEAD synced from the current
+// checkout, yields to the listed candidate.
+export function resolveWorktreeBaseBranchSeed(input: {
+  activeThreadBranch: string | null;
+  activeThreadBranchListed: boolean | null;
+  refs: ReadonlyArray<VcsRef>;
+}): string | null {
+  if (input.activeThreadBranch !== null && input.activeThreadBranchListed !== false) return null;
+  const { refs } = input;
+  return (refs.find((ref) => ref.isDefault) ?? refs.find((ref) => ref.current))?.name ?? null;
+}
+
 export function resolveBranchToolbarValue(input: {
   envMode: EnvMode;
   activeWorktreePath: string | null;
diff --git a/apps/web/src/components/BranchToolbarBranchSelector.tsx b/apps/web/src/components/BranchToolbarBranchSelector.tsx
index da845e95fc0b..bde3be59315b 100644
--- a/apps/web/src/components/BranchToolbarBranchSelector.tsx
+++ b/apps/web/src/components/BranchToolbarBranchSelector.tsx
@@ -19,6 +19,7 @@ import {
 import { GitBranchIcon } from "lucide-react";
 import {
   useEffect,
+  useEffectEvent,
   useImperativeHandle,
   useOptimistic,
   useState,
@@ -33,6 +34,7 @@ import { readLocalApi } from "../localApi";
 import { useOpenPrLink } from "../lib/openPullRequestLink";
 import { usePaginatedBranches } from "../state/queries";
 import { readThreadShell, useProject, useQuietThreadShell } from "../state/entities";
+import { useProjectClone } from "../state/projectClones";
 import { useEnvironmentQuery } from "../state/query";
 import { readEnvironmentScope, useEnvironmentScope } from "~/state/session";
 import { threadEnvironment } from "../state/threads";
@@ -53,6 +55,7 @@ import {
   resolveBranchToolbarValue,
   resolveDraftEnvModeAfterBranchChange,
   resolveEffectiveEnvMode,
+  resolveWorktreeBaseBranchSeed,
   sanitizeNewRefName,
   shouldIncludeBranchPickerItem,
 } from "./BranchToolbar.logic";
@@ -264,6 +267,16 @@ export function BranchToolbarBranchSelector({
     query: sanitizeNewRefName(trimmedBranchQuery),
   });
   const refs = branchRefState.refs;
+  const isProjectCloneDone = useProjectClone(activeProjectRef)?.phase === "done";
+  // An Effect Event: refreshStatus is a new closure each render, and its settlement re-renders us.
+  const refreshClonedBranchStatus = useEffectEvent((target: EnvironmentId, cwd: string) => {
+    void refreshStatus({ environmentId: target, input: { cwd, localOnly: true } });
+  });
+  // oxlint-disable-next-line t3code/no-unreasoned-state-sync -- refs listed while the project was cloning are empty; refetch them from the server once the clone lands
+  useEffect(() => {
+    if (!isProjectCloneDone || branchCwd === null) return;
+    refreshClonedBranchStatus(environmentId, branchCwd);
+  }, [branchCwd, environmentId, isProjectCloneDone]);
   const branchByName = new Map(refs.map((refName) => [refName.name, refName] as const));
   const normalizedBranchQuery = trimmedBranchQuery.toLowerCase();
   const prReference = parsePullRequestReference(trimmedBranchQuery);
@@ -294,7 +307,6 @@ export function BranchToolbarBranchSelector({
   const createBranchItemValue = canCreateBranch
     ? `__create_new_branch__:${trimmedBranchQuery}`
     : null;
-  const defaultBranchName = refs.find((refName) => refName.isDefault)?.name ?? null;
   const pickerCreateBranchItemValue = hasExactBranchMatch ? null : createBranchItemValue;
   const branchPickerItems = [
     ...(checkoutPullRequestItemValue ? [checkoutPullRequestItemValue] : []),
@@ -536,9 +548,17 @@ export function BranchToolbarBranchSelector({
     });
   };
 
-  const worktreeBaseBranchCandidate = isInitialBranchesLoadPending
+  const activeThreadBranchListed =
+    activeThreadBranch === null || activeThreadBranch !== resolvedActiveBranch
+      ? null
+      : listedActiveBranch !== null || queriedActiveBranch !== undefined
+        ? true
+        : activeBranchRefQuery.data !== null
+          ? false
+          : null;
+  const worktreeBaseBranchSeed = isInitialBranchesLoadPending
     ? null
-    : (defaultBranchName ?? currentGitBranch);
+    : resolveWorktreeBaseBranchSeed({ activeThreadBranch, activeThreadBranchListed, refs });
 
   // The server sets started threads' branches; defaulting here would detach the agent from its worktree.
   const threadStarted = serverSession !== null;
@@ -548,19 +568,17 @@ export function BranchToolbarBranchSelector({
       threadStarted ||
       effectiveEnvMode !== "worktree" ||
       activeWorktreePath ||
-      activeThreadBranch ||
-      !worktreeBaseBranchCandidate
+      !worktreeBaseBranchSeed
     ) {
       return;
     }
-    setThreadBranch(worktreeBaseBranchCandidate, null, true);
+    setThreadBranch(worktreeBaseBranchSeed, null, true);
   }, [
-    activeThreadBranch,
     activeWorktreePath,
     effectiveEnvMode,
     setThreadBranch,
     threadStarted,
-    worktreeBaseBranchCandidate,
+    worktreeBaseBranchSeed,
   ]);
 
   const handleOpenChange = (open: boolean) => {