diff --git a/apps/web/src/components/CommandPalette.logic.test.ts b/apps/web/src/components/CommandPalette.logic.test.ts
index 8cf712b113cf7..5295d27c67ba5 100644
--- a/apps/web/src/components/CommandPalette.logic.test.ts
+++ b/apps/web/src/components/CommandPalette.logic.test.ts
@@ -9,6 +9,7 @@ import {
   buildLinkedThreadActionItems,
   filterPinnedBrowseEntries,
   filterCommandPaletteGroups,
+  resolveNewThreadProjectGroups,
   reduceCommandPaletteUiState,
   resolveAddProjectEntry,
   createCommandPaletteSearchState,
@@ -920,6 +921,48 @@ describe("returning from file and content search", () => {
   });
 });
 
+describe("open new-thread project choices", () => {
+  it("uses current choices and actions while preserving other submenus", async () => {
+    const staleRun = vi.fn(async () => undefined);
+    const currentRun = vi.fn(async () => undefined);
+    const action = (value: string, run = staleRun) => ({
+      kind: "action" as const,
+      value,
+      title: value,
+      searchTerms: [value],
+      icon: null,
+      run,
+    });
+    const stored = [
+      {
+        value: "new-thread-in",
+        label: "Projects",
+        items: [action("scratch"), action("checkout-a"), action("checkout-b")],
+      },
+    ];
+    const current = [action("grouped-repository"), action("arriving-project", currentRun)];
+    const groups = resolveNewThreadProjectGroups(stored, current);
+    const visible = filterCommandPaletteGroups({
+      activeGroups: groups,
+      query: "",
+      isInSubmenu: true,
+      projectSearchItems: [],
+      threadSearchItems: [],
+    });
+    expect(visible.flatMap((group) => group.items.map((item) => item.title))).toEqual([
+      "grouped-repository",
+      "arriving-project",
+    ]);
+    const arriving = visible[0]!.items[1]!;
+    if (arriving.kind !== "action") throw new Error("Expected a project action");
+    await arriving.run();
+    expect(currentRun).toHaveBeenCalledOnce();
+    expect(staleRun).not.toHaveBeenCalled();
+    const other = [{ ...stored[0]!, value: "projects" }];
+    expect(resolveNewThreadProjectGroups(other, current)).toBe(other);
+  });
+});
+
 it("resolves project metadata and browse roots within the active environment", () => {
   const local = { title: "Local project", workspaceRoot: "/local/repo" };
   const remote = { title: "Remote project", workspaceRoot: "/remote/repo" };
diff --git a/apps/web/src/components/CommandPalette.logic.ts b/apps/web/src/components/CommandPalette.logic.ts
index 96d439252ac53..d2f455dbd55fd 100644
--- a/apps/web/src/components/CommandPalette.logic.ts
+++ b/apps/web/src/components/CommandPalette.logic.ts
@@ -223,6 +223,13 @@ export interface CommandPaletteGroup {
   readonly items: ReadonlyArray<CommandPaletteActionItem | CommandPaletteSubmenuItem>;
 }
 
+export function resolveNewThreadProjectGroups(
+  groups: ReadonlyArray<CommandPaletteGroup>,
+  items: ReadonlyArray<CommandPaletteActionItem>,
+): ReadonlyArray<CommandPaletteGroup> {
+  return groups[0]?.value === "new-thread-in" ? [{ ...groups[0], items }] : groups;
+}
+
 export interface CommandPaletteView {
   readonly addonIcon: ReactNode;
   readonly groups: ReadonlyArray<CommandPaletteGroup>;
diff --git a/apps/web/src/components/CommandPalette.tsx b/apps/web/src/components/CommandPalette.tsx
index deb9092726641..b0111a3d2aadf 100644
--- a/apps/web/src/components/CommandPalette.tsx
+++ b/apps/web/src/components/CommandPalette.tsx
@@ -175,6 +175,7 @@ import {
   type CommandPaletteSubmenuItem,
   type CommandPaletteView,
   filterCommandPaletteGroups,
+  resolveNewThreadProjectGroups,
   buildNestedSearchItems,
   filterPinnedBrowseEntries,
   getCommandPaletteInputPlaceholder,
@@ -244,7 +245,7 @@ import { threadRecentUse } from "@t3tools/shared/paletteSearch";
 
 const EMPTY_BROWSE_ENTRIES: FilesystemBrowseResult["entries"] = [];
 const ADD_PROJECT_ENTRY_GROUP = "add-project";
-const NEW_THREAD_IN_GROUP = "projects";
+const NEW_THREAD_IN_GROUP = "new-thread-in";
 
 /** The submenu an open intent starts in; its groups resolve while rendering. */
 function openIntentView(intent: CommandPaletteOpenIntent | null): CommandPaletteView | null {
@@ -1607,18 +1608,16 @@ function OpenCommandPaletteDialog(props: {
         )
       : currentView?.groups[0]?.value === ADD_PROJECT_ENTRY_GROUP
         ? addProjectEntryGroups()
-        : currentView?.groups[0]?.value === NEW_THREAD_IN_GROUP
-          ? [{ value: NEW_THREAD_IN_GROUP, label: "Projects", items: projectThreadItems }]
-          : currentView?.groups[0]?.value === "themes"
-            ? changeThemeItem.groups
-            : currentView?.groups[0]?.value === "appearance"
-              ? changeAppearanceItem.groups
-              : (currentView?.groups ?? rootGroups);
+        : currentView?.groups[0]?.value === "themes"
+          ? changeThemeItem.groups
+          : currentView?.groups[0]?.value === "appearance"
+            ? changeAppearanceItem.groups
+            : (currentView?.groups ?? rootGroups);
 
   const isLinkedThreadSearch =
     linkedThreadSearch?.linkedThreads !== undefined && deferredQuery === linkedThreadSearch.query;
   const filteredGroups = filterCommandPaletteGroups({
-    activeGroups,
+    activeGroups: resolveNewThreadProjectGroups(activeGroups, projectThreadItems),
     query: deferredQuery,
     isInSubmenu: currentView !== null,
     ...(deferredQuery.trim().length > 0