diff --git a/.changeset/agent-manager-latest-selection.md b/.changeset/agent-manager-latest-selection.md
new file mode 100644
index 000000000000..c5f144ad2618
--- /dev/null
+++ b/.changeset/agent-manager-latest-selection.md
@@ -0,0 +1,5 @@
+---
+"kilo-code": patch
+---
+
+Keep the latest Agent Manager selection when another project finishes loading.
diff --git a/packages/kilo-vscode/src/agent-manager/project/messages.ts b/packages/kilo-vscode/src/agent-manager/project/messages.ts
index 34c798a4bdeb..0a7a60a02683 100644
--- a/packages/kilo-vscode/src/agent-manager/project/messages.ts
+++ b/packages/kilo-vscode/src/agent-manager/project/messages.ts
@@ -18,6 +18,7 @@ import { cloneProject, createProject, defaultParent, onboard, type Onboarding }
 import { runner } from "./prepare"
 
 const pending = new WeakSet<ProjectMessageDeps>()
+const selections = new WeakMap<ProjectMessageDeps, symbol>()
 
 /** Route one session to a directory inside a project via the shared session provider. */
 export function routeProjectSession(
@@ -138,7 +139,13 @@ async function activateSelection(requested: SidebarTarget, deps: ProjectMessageD
     deps.error("The project is unavailable. Check that the repository still exists.")
     return
   }
+  // Record the token only for an actionable target, so a click on an
+  // unavailable project cannot discard a pending valid selection.
+  const token = Symbol()
+  selections.set(deps, token)
   const result = await deps.ready(ctx, { warm: true })
+  // A newer click can finish while this project's readiness is pending.
+  if (selections.get(deps) !== token || !deps.enabled()) return
   if (!result.current || !result.ok) {
     deps.error("The project is not ready yet. Expand it before selecting a worktree or session.")
     deps.push()
diff --git a/packages/kilo-vscode/tests/unit/agent-project-selection.test.ts b/packages/kilo-vscode/tests/unit/agent-project-selection.test.ts
index 70fa285b5b36..610eb716f6c0 100644
--- a/packages/kilo-vscode/tests/unit/agent-project-selection.test.ts
+++ b/packages/kilo-vscode/tests/unit/agent-project-selection.test.ts
@@ -131,6 +131,53 @@ describe("activateSelection — cross-project selection", () => {
     expect(calls.selected).toEqual([extra])
   })
 
+  it.each([true, false])("ignores a superseded selection when readiness completes with ok=%s", async (ok) => {
+    const gate = Promise.withResolvers<void>()
+    const { contexts, deps, calls, extra } = setup({
+      ready: (ctx) =>
+        ctx.ensureReady(async () => {
+          ctx.stateManager()
+          if (!ctx.pinned) await gate.promise
+          return { ok: ctx.pinned || ok, refsFixed: 0 }
+        }),
+    })
+
+    const pending = handleProjectMessage(activateMsg(extra), deps)
+    await handleProjectMessage(activateMsg(PINNED, { kind: "worktree", worktreeId: "wt1" }), deps)
+    expect(calls.selected).toEqual(["worktree"])
+
+    gate.resolve()
+    await pending
+
+    expect(contexts.active()?.id).toBe(PINNED)
+    expect(calls.selected).toEqual(["worktree"])
+    expect(contexts.get(extra)?.peekState()?.getActiveTarget()).toBeUndefined()
+    expect(calls.error).toEqual([])
+  })
+
+  it("keeps a pending selection when a newer click targets an unavailable project", async () => {
+    const gate = Promise.withResolvers<void>()
+    const { contexts, deps, calls, extra } = setup({
+      ready: (ctx) =>
+        ctx.ensureReady(async () => {
+          ctx.stateManager()
+          if (!ctx.pinned) await gate.promise
+          return { ok: true, refsFixed: 0 }
+        }),
+    })
+
+    const pending = handleProjectMessage(activateMsg(extra), deps)
+    await handleProjectMessage(activateMsg("prj-missing"), deps)
+    expect(calls.selected).toEqual([])
+    expect(calls.error.length).toBe(1)
+
+    gate.resolve()
+    await pending
+
+    expect(contexts.active()?.id).toBe(extra)
+    expect(calls.selected).toEqual([extra])
+  })
+
   it("falls back to local without an error toast when the target is gone", async () => {
     const { contexts, deps, calls, extra } = setup()
     contexts.activate(PINNED)