diff --git a/packages/desktop/src/main/deep-links/index.ts b/packages/desktop/src/main/deep-links/index.ts
new file mode 100644
index 00000000000..ccd9b1e39b1
--- /dev/null
+++ b/packages/desktop/src/main/deep-links/index.ts
@@ -0,0 +1,52 @@
+export * as DeepLinks from "./index"
+
+import type { BrowserWindow } from "electron"
+import { Effect } from "effect"
+import { DeepLinksOpened } from "../../shared/ipc-rpc/events"
+import { emitIpcEvent } from "../ipc-events"
+import { getWindowByID, onMainWindow } from "../windows"
+import { createDeepLinkState, transitionDeepLinks, type DeepLinkEvent } from "./machine"
+
+export interface Interface {
+  readonly receive: (urls: readonly string[]) => void
+  readonly ready: (windowID: string, clientID: number) => void
+  readonly acknowledge: (clientID: number, attempt: number) => void
+  readonly disconnect: (clientID: number) => void
+}
+
+/** Routes deep links to app windows through the delivery machine for as long as the caller's scope lives. */
+export const make = Effect.fn("DeepLinks.make")(function* (focus: (win: BrowserWindow | null) => void) {
+  let state = createDeepLinkState()
+
+  const dispatch = (event: DeepLinkEvent): void => {
+    const next = transitionDeepLinks(state, event)
+    // Commit before running commands: focusing a window dispatches its focus event synchronously.
+    state = next.state
+    next.commands.forEach((command) => {
+      if (command.type === "window.focus") return focus(getWindowByID(command.windowID))
+      const win = getWindowByID(command.windowID)
+      const opened = new DeepLinksOpened({ attempt: command.attempt, urls: command.urls })
+      const sent = !!win && emitIpcEvent(win.webContents, opened)
+
+      // A renderer without an event stream is gone, so its links wait for the next one.
+      if (!sent) dispatch({ type: "client.disconnected", clientID: command.clientID })
+    })
+  }
+
+  const stop = onMainWindow((win, windowID) => {
+    dispatch({ type: "window.opened", windowID })
+
+    if (win.isFocused()) dispatch({ type: "window.focused", windowID })
+    win.on("focus", () => dispatch({ type: "window.focused", windowID }))
+    win.once("closed", () => dispatch({ type: "window.closed", windowID }))
+  })
+
+  yield* Effect.addFinalizer(() => Effect.sync(stop))
+
+  return {
+    receive: (urls) => dispatch({ type: "links.received", urls }),
+    ready: (windowID, clientID) => dispatch({ type: "window.ready", windowID, clientID }),
+    acknowledge: (clientID, attempt) => dispatch({ type: "delivery.acknowledged", clientID, attempt }),
+    disconnect: (clientID) => dispatch({ type: "client.disconnected", clientID }),
+  } satisfies Interface
+})
diff --git a/packages/desktop/src/main/deep-links/machine.test.ts b/packages/desktop/src/main/deep-links/machine.test.ts
new file mode 100644
index 00000000000..263286efcd4
--- /dev/null
+++ b/packages/desktop/src/main/deep-links/machine.test.ts
@@ -0,0 +1,168 @@
+import { describe, expect, test } from "bun:test"
+import {
+  createDeepLinkState,
+  transitionDeepLinks,
+  type DeepLinkCommand,
+  type DeepLinkEvent,
+  type DeepLinkState,
+} from "./machine"
+
+const oauth = "opencode://console/authorized?window=a"
+
+const oauthB = "opencode://console/authorized?window=b"
+
+const project = "opencode://open?project=/repo"
+
+// Folds events through the machine and keeps the commands of each step.
+function replay(events: readonly DeepLinkEvent[], from = createDeepLinkState()) {
+  return events.reduce<{ state: DeepLinkState; commands: (readonly DeepLinkCommand[])[] }>(
+    (result, event) => {
+      const next = transitionDeepLinks(result.state, event)
+
+      return { state: next.state, commands: [...result.commands, next.commands] }
+    },
+    { state: from, commands: [] },
+  )
+}
+
+const ready = (windowID: string, clientID: number): DeepLinkEvent[] => [
+  { type: "window.opened", windowID },
+  { type: "window.ready", windowID, clientID },
+]
+
+describe("deep link delivery", () => {
+  test("never hands an acknowledged link to a reloaded or new window", () => {
+    const live = replay([
+      ...ready("a", 1),
+      { type: "window.focused", windowID: "a" },
+      { type: "links.received", urls: [oauth, project] },
+    ])
+
+    expect(live.commands.at(-1)).toEqual([
+      { type: "links.deliver", windowID: "a", clientID: 1, attempt: 1, urls: [oauth, project] },
+      { type: "window.focus", windowID: "a" },
+    ])
+
+    // View > Reload, then a new window: on dev both booted renderers drained the shared queue again.
+    const after = replay(
+      [
+        { type: "delivery.acknowledged", clientID: 1, attempt: 1 },
+        { type: "client.disconnected", clientID: 1 },
+        { type: "window.ready", windowID: "a", clientID: 2 },
+        ...ready("b", 3),
+      ],
+      live.state,
+    )
+
+    expect(after.commands.flat()).toEqual([])
+    expect(after.state.links).toEqual([])
+  })
+
+  test("queues a link until the first window is ready", () => {
+    const result = replay([{ type: "links.received", urls: [project] }, { type: "window.opened", windowID: "a" }])
+    expect(result.commands.flat()).toEqual([])
+    expect(result.state.links).toEqual([{ status: "queued", url: project, target: undefined }])
+
+    expect(transitionDeepLinks(result.state, { type: "window.ready", windowID: "a", clientID: 1 }).commands).toEqual([
+      { type: "links.deliver", windowID: "a", clientID: 1, attempt: 1, urls: [project] },
+    ])
+  })
+
+  test("waits for the window a console return names instead of the focused one", () => {
+    const result = replay([
+      { type: "window.opened", windowID: "a" },
+      ...ready("b", 2),
+      { type: "window.focused", windowID: "b" },
+      { type: "links.received", urls: [oauth] },
+    ])
+
+    expect(result.commands.at(-1)).toEqual([{ type: "window.focus", windowID: "a" }])
+
+    expect(transitionDeepLinks(result.state, { type: "window.ready", windowID: "a", clientID: 1 }).commands).toEqual([
+      { type: "links.deliver", windowID: "a", clientID: 1, attempt: 1, urls: [oauth] },
+    ])
+  })
+
+  test("splits one arrival into a batch and attempt per window", () => {
+    const result = replay([
+      ...ready("b", 2),
+      ...ready("c", 3),
+      { type: "window.focused", windowID: "c" },
+      { type: "links.received", urls: [project, oauthB] },
+    ])
+
+    expect(result.commands.at(-1)).toEqual([
+      { type: "links.deliver", windowID: "c", clientID: 3, attempt: 1, urls: [project] },
+      { type: "links.deliver", windowID: "b", clientID: 2, attempt: 2, urls: [oauthB] },
+      { type: "window.focus", windowID: "b" },
+    ])
+  })
+
+  test("delivers an unacknowledged link again to the next renderer and ignores stale replies", () => {
+    const delivered = replay([...ready("a", 1), { type: "links.received", urls: [project] }])
+
+    const reloaded = replay(
+      [
+        { type: "client.disconnected", clientID: 1 },
+        { type: "window.ready", windowID: "a", clientID: 2 },
+      ],
+      delivered.state,
+    )
+
+    expect(reloaded.commands).toEqual([
+      [],
+      [{ type: "links.deliver", windowID: "a", clientID: 2, attempt: 2, urls: [project] }],
+    ])
+
+    const stale: DeepLinkEvent[] = [
+      { type: "delivery.acknowledged", clientID: 1, attempt: 1 },
+      { type: "delivery.acknowledged", clientID: 2, attempt: 1 },
+      { type: "delivery.acknowledged", clientID: 1, attempt: 2 },
+      { type: "client.disconnected", clientID: 1 },
+      { type: "window.ready", windowID: "a", clientID: 2 },
+    ]
+
+    stale.forEach((event) => {
+      const next = transitionDeepLinks(reloaded.state, event)
+      expect(next.state).toBe(reloaded.state)
+      expect(next.commands).toEqual([])
+    })
+  })
+
+  test("sends links for a closed window to the focused one, as before", () => {
+    const result = replay([
+      { type: "window.opened", windowID: "a" },
+      ...ready("b", 2),
+      { type: "links.received", urls: [oauth] },
+      { type: "window.closed", windowID: "a" },
+    ])
+
+    expect(result.commands.at(-1)).toEqual([
+      { type: "links.deliver", windowID: "b", clientID: 2, attempt: 1, urls: [oauth] },
+    ])
+  })
+
+  test("follows focus to a ready window while the focused one loads", () => {
+    const result = replay([
+      { type: "window.opened", windowID: "a" },
+      { type: "window.focused", windowID: "a" },
+      ...ready("b", 2),
+      { type: "links.received", urls: [project] },
+      { type: "window.focused", windowID: "b" },
+    ])
+
+    expect(result.commands.at(-2)).toEqual([{ type: "window.focus", windowID: "a" }])
+    expect(result.commands.at(-1)).toEqual([
+      { type: "links.deliver", windowID: "b", clientID: 2, attempt: 1, urls: [project] },
+    ])
+  })
+
+  test("adopts a window whose renderer reports ready before it registers", () => {
+    const result = replay([
+      { type: "window.ready", windowID: "a", clientID: 1 },
+      { type: "window.opened", windowID: "a" },
+    ])
+
+    expect(result.state.windows).toEqual({ a: { status: "ready", clientID: 1 } })
+  })
+})
diff --git a/packages/desktop/src/main/deep-links/machine.ts b/packages/desktop/src/main/deep-links/machine.ts
new file mode 100644
index 00000000000..0ef982042d6
--- /dev/null
+++ b/packages/desktop/src/main/deep-links/machine.ts
@@ -0,0 +1,198 @@
+import { consoleReturnWindow } from "../lifecycle/deep-link"
+
+export type DeepLinkWindow = { readonly status: "loading" } | { readonly status: "ready"; readonly clientID: number }
+
+// `target` is the window a console return names; a link without one, or whose window is gone, opens in the
+// preferred window.
+export type DeepLink =
+  | { readonly status: "queued"; readonly url: string; readonly target: string | undefined }
+  | {
+      readonly status: "delivered"
+      readonly url: string
+      readonly target: string | undefined
+      readonly clientID: number
+      readonly attempt: number
+    }
+
+export type DeepLinkState = {
+  readonly windows: Readonly<Record<string, DeepLinkWindow>>
+  readonly focusedWindowID: string | undefined
+  readonly links: readonly DeepLink[]
+  readonly nextAttempt: number
+}
+
+export type DeepLinkEvent =
+  | { readonly type: "links.received"; readonly urls: readonly string[] }
+  | { readonly type: "window.opened"; readonly windowID: string }
+  | { readonly type: "window.focused"; readonly windowID: string }
+  | { readonly type: "window.ready"; readonly windowID: string; readonly clientID: number }
+  | { readonly type: "window.closed"; readonly windowID: string }
+  | { readonly type: "client.disconnected"; readonly clientID: number }
+  | { readonly type: "delivery.acknowledged"; readonly clientID: number; readonly attempt: number }
+
+export type DeepLinkCommand =
+  | {
+      readonly type: "links.deliver"
+      readonly windowID: string
+      readonly clientID: number
+      readonly attempt: number
+      readonly urls: readonly string[]
+    }
+  | { readonly type: "window.focus"; readonly windowID: string }
+
+export type DeepLinkTransition = {
+  readonly state: DeepLinkState
+  readonly commands: readonly DeepLinkCommand[]
+}
+
+export function createDeepLinkState(): DeepLinkState {
+  return { windows: {}, focusedWindowID: undefined, links: [], nextAttempt: 1 }
+}
+
+export function transitionDeepLinks(state: DeepLinkState, event: DeepLinkEvent): DeepLinkTransition {
+  switch (event.type) {
+    case "links.received": {
+      if (event.urls.length === 0) return unchanged(state)
+      const links = event.urls.map((url): DeepLink => ({ status: "queued", url, target: consoleReturnWindow(url) }))
+      const focus = links.find((link) => link.target && state.windows[link.target])?.target ?? preferredWindowID(state)
+      const next = drain({ ...state, links: [...state.links, ...links] })
+
+      return {
+        state: next.state,
+        commands: focus ? [...next.commands, { type: "window.focus", windowID: focus }] : next.commands,
+      }
+    }
+
+    case "window.opened": {
+      if (state.windows[event.windowID]) return unchanged(state)
+
+      return drain({ ...state, windows: { ...state.windows, [event.windowID]: { status: "loading" } } })
+    }
+
+    case "window.focused": {
+      if (!state.windows[event.windowID] || state.focusedWindowID === event.windowID) return unchanged(state)
+
+      return drain({ ...state, focusedWindowID: event.windowID })
+    }
+
+    case "window.ready": {
+      const current = state.windows[event.windowID]
+
+      if (current?.status === "ready" && current.clientID === event.clientID) return unchanged(state)
+
+      return drain({
+        ...state,
+        windows: { ...state.windows, [event.windowID]: { status: "ready", clientID: event.clientID } },
+        links: current?.status === "ready" ? requeue(state.links, current.clientID) : state.links,
+      })
+    }
+
+    case "window.closed": {
+      const current = state.windows[event.windowID]
+
+      if (!current) return unchanged(state)
+
+      return drain({
+        ...state,
+        windows: Object.fromEntries(Object.entries(state.windows).filter(([id]) => id !== event.windowID)),
+        focusedWindowID: state.focusedWindowID === event.windowID ? undefined : state.focusedWindowID,
+        links: current.status === "ready" ? requeue(state.links, current.clientID) : state.links,
+      })
+    }
+
+    case "client.disconnected": {
+      const windowID = Object.entries(state.windows).find(
+        ([, window]) => window.status === "ready" && window.clientID === event.clientID,
+      )?.[0]
+
+      const delivered = state.links.some((link) => link.status === "delivered" && link.clientID === event.clientID)
+
+      if (!windowID && !delivered) return unchanged(state)
+
+      return drain({
+        ...state,
+        windows: windowID ? { ...state.windows, [windowID]: { status: "loading" } } : state.windows,
+        links: requeue(state.links, event.clientID),
+      })
+    }
+
+    case "delivery.acknowledged": {
+      // An acknowledged link leaves the state, so no later renderer can receive it again.
+      const links = state.links.filter(
+        (link) => link.status !== "delivered" || link.clientID !== event.clientID || link.attempt !== event.attempt,
+      )
+
+      if (links.length === state.links.length) return unchanged(state)
+
+      return { state: { ...state, links }, commands: [] }
+    }
+  }
+}
+
+// The window an untargeted link opens in: the focused one, else the first open one.
+function preferredWindowID(state: DeepLinkState) {
+  return state.focusedWindowID ?? Object.keys(state.windows)[0]
+}
+
+// The ready window and renderer a link goes to now, if any.
+function recipientOf(state: DeepLinkState, link: DeepLink) {
+  const windowID = link.target && state.windows[link.target] ? link.target : preferredWindowID(state)
+  const window = windowID ? state.windows[windowID] : undefined
+
+  if (!windowID || window?.status !== "ready") return
+
+  return { windowID, clientID: window.clientID }
+}
+
+// Sends every queued link whose window is ready, one batch and attempt per window.
+function drain(state: DeepLinkState): DeepLinkTransition {
+  const routed = state.links.map((link) => ({
+    link,
+    recipient: link.status === "queued" ? recipientOf(state, link) : undefined,
+  }))
+
+  const recipients = routed.flatMap((item) => (item.recipient ? [item.recipient] : []))
+
+  const batches = recipients
+    .filter((recipient, index) => recipients.findIndex((other) => other.windowID === recipient.windowID) === index)
+    .map((recipient, index) => ({
+      ...recipient,
+      attempt: state.nextAttempt + index,
+      urls: routed.flatMap((item) => (item.recipient?.windowID === recipient.windowID ? [item.link.url] : [])),
+    }))
+
+  if (batches.length === 0) return { state, commands: [] }
+
+  const links = routed.map((item): DeepLink => {
+    const batch = batches.find((candidate) => candidate.windowID === item.recipient?.windowID)
+
+    if (!batch) return item.link
+
+    return {
+      status: "delivered",
+      url: item.link.url,
+      target: item.link.target,
+      clientID: batch.clientID,
+      attempt: batch.attempt,
+    }
+  })
+
+  return {
+    state: { ...state, links, nextAttempt: state.nextAttempt + batches.length },
+    commands: batches.map((batch): DeepLinkCommand => ({ type: "links.deliver", ...batch })),
+  }
+}
+
+// A renderer that went away without acknowledging may not have handled its links, so they wait for the next one.
+function requeue(links: readonly DeepLink[], clientID: number) {
+  return links.map(
+    (link): DeepLink =>
+      link.status === "delivered" && link.clientID === clientID
+        ? { status: "queued", url: link.url, target: link.target }
+        : link,
+  )
+}
+
+function unchanged(state: DeepLinkState): DeepLinkTransition {
+  return { state, commands: [] }
+}
diff --git a/packages/desktop/src/main/ipc-events.ts b/packages/desktop/src/main/ipc-events.ts
index c1119b80c4d..ad5d4e73861 100644
--- a/packages/desktop/src/main/ipc-events.ts
+++ b/packages/desktop/src/main/ipc-events.ts
@@ -23,8 +23,9 @@ export function ipcEventStream(senderId: number) {
   return queue ? Stream.fromQueue(queue) : Stream.empty
 }
 
+/** Returns false when the renderer has no event stream to receive the event. */
 export function emitIpcEvent(sender: WebContents, event: DesktopEvent) {
   const queue = queues.get(sender.id)
 
-  if (queue) Queue.offerUnsafe(queue, event)
+  return queue ? Queue.offerUnsafe(queue, event) : false
 }
diff --git a/packages/desktop/src/main/ipc-handlers/app.ts b/packages/desktop/src/main/ipc-handlers/app.ts
index c2542481484..ba13c4807fe 100644
--- a/packages/desktop/src/main/ipc-handlers/app.ts
+++ b/packages/desktop/src/main/ipc-handlers/app.ts
@@ -16,7 +16,7 @@ import { finishFirstLaunchOnboarding, isFirstLaunchOnboardingPending } from "../
 import { BackgroundService } from "../service/background-service"
 import { DesktopCli } from "../service/desktop-cli"
 import { SidecarCredentials } from "../service/sidecar-credentials"
-import { getLastFocusedWindow, setBackgroundColor } from "../windows"
+import { getLastFocusedWindow, getWindowID, setBackgroundColor } from "../windows"
 import { sender } from "./context"
 
 export const appHandlers = AppRpcs.toLayer(
@@ -31,7 +31,17 @@ export const appHandlers = AppRpcs.toLayer(
     return AppRpcs.of({
       AppAwaitInitialization: () => background.connection.pipe(Effect.map(SidecarCredentials.ready)),
       AppReconnectService: () => background.reconnect.pipe(Effect.map(SidecarCredentials.ready)),
-      AppConsumeInitialDeepLinks: () => Effect.sync(lifecycle.consumeInitialDeepLinks),
+      AppReadyDeepLinks: (_request, context) =>
+        Effect.sync(() => {
+          const contents = sender(handoff, context)
+          const win = BrowserWindow.fromWebContents(contents)
+          // Only an app window's own renderer receives deep links, not one embedded in it.
+          const id = win?.webContents === contents ? getWindowID(win) : undefined
+
+          if (id) lifecycle.deepLinks.ready(id, context.client.id)
+        }),
+      AppAcknowledgeDeepLinks: ({ attempt }, context) =>
+        Effect.sync(() => lifecycle.deepLinks.acknowledge(context.client.id, attempt)),
       AppIsFirstLaunchOnboardingPending: isFirstLaunchOnboardingPending,
       AppFinishFirstLaunchOnboarding: ({ createDefaultProject }) =>
         finishFirstLaunchOnboarding(createDefaultProject).pipe(Effect.orDie),
diff --git a/packages/desktop/src/main/ipc-transport.test.ts b/packages/desktop/src/main/ipc-transport.test.ts
index a4d29eb70a5..5274ffe14a4 100644
--- a/packages/desktop/src/main/ipc-transport.test.ts
+++ b/packages/desktop/src/main/ipc-transport.test.ts
@@ -77,6 +77,8 @@ describe("desktop RPC transport", () => {
     const live = RpcServer.layer(TestRpcs).pipe(Layer.provide(handlers), Layer.provideMerge(IpcServerProtocolLive))
     const runtime = ManagedRuntime.make(live)
     const handoff = await runtime.runPromise(IpcPortHandoff)
+    const disconnected: number[] = []
+    handoff.onDisconnect((clientId) => disconnected.push(clientId))
     const first = new MessageChannel()
     const second = new MessageChannel()
     handoff.bind(sender(1), serverPort(first.port1))
@@ -108,6 +110,8 @@ describe("desktop RPC transport", () => {
 
     expect(reloadedFocused.exit).toEqual(success(true))
     expect(stillUnfocused.exit).toEqual(success(false))
+    // Deep link delivery returns unacknowledged links to the queue when a reload replaces a renderer's port.
+    expect(disconnected).toEqual([0])
 
     for (const port of [first.port2, second.port2, reloaded.port2]) port.close()
     await runtime.dispose()
diff --git a/packages/desktop/src/main/ipc-transport.ts b/packages/desktop/src/main/ipc-transport.ts
index 3287d2a99f1..0797494e856 100644
--- a/packages/desktop/src/main/ipc-transport.ts
+++ b/packages/desktop/src/main/ipc-transport.ts
@@ -15,6 +15,8 @@ type PortBinding = {
 type Handoff = {
   readonly bind: (sender: WebContents, port: MessagePortMain) => void
   readonly sender: (clientId: number) => WebContents | undefined
+  /** Runs after a renderer port closes or is replaced, before a replacement port for its sender binds. */
+  readonly onDisconnect: (listener: (clientId: number) => void) => () => void
 }
 
 export class IpcPortHandoff extends Context.Service<IpcPortHandoff, Handoff>()("opencode/desktop/IpcPortHandoff") {}
@@ -27,6 +29,7 @@ export const IpcServerProtocolLive = Layer.unwrap(
     const handoffs = yield* Queue.unbounded<readonly [WebContents, MessagePortMain]>()
     const bindings = new Map<number, PortBinding>()
     const senderBindings = new Map<number, number>()
+    const disconnected = new Set<(clientId: number) => void>()
 
     const protocol = Layer.effect(
       RpcServer.Protocol,
@@ -49,6 +52,7 @@ export const IpcServerProtocolLive = Layer.unwrap(
             binding.sender.off("destroyed", binding.onClose)
             yield* binding.unbindEvents
             binding.port.close()
+            disconnected.forEach((listener) => listener(id))
             Queue.offerUnsafe(disconnects, id)
           })
 
@@ -118,6 +122,13 @@ export const IpcServerProtocolLive = Layer.unwrap(
           Queue.offerUnsafe(handoffs, [sender, port])
         },
         sender: (clientId) => bindings.get(clientId)?.sender,
+        onDisconnect: (listener) => {
+          disconnected.add(listener)
+
+          return () => {
+            disconnected.delete(listener)
+          }
+        },
       }),
     )
   }),
diff --git a/packages/desktop/src/main/ipc.ts b/packages/desktop/src/main/ipc.ts
index 6c68d43357b..cdf35dbee1c 100644
--- a/packages/desktop/src/main/ipc.ts
+++ b/packages/desktop/src/main/ipc.ts
@@ -82,6 +82,8 @@ export const registerIpcHandlers = Effect.gen(function* () {
   }
 
   const onWindowCreated = (_event: Electron.Event, win: BrowserWindow) => wire(win)
+  const stopDisconnects = handoff.onDisconnect(lifecycle.deepLinks.disconnect)
+  yield* Effect.addFinalizer(() => Effect.sync(stopDisconnects))
 
   yield* Effect.sync(() => {
     app.on("browser-window-created", onWindowCreated)
diff --git a/packages/desktop/src/main/lifecycle/index.ts b/packages/desktop/src/main/lifecycle/index.ts
index df043c9b96f..5274113a220 100644
--- a/packages/desktop/src/main/lifecycle/index.ts
+++ b/packages/desktop/src/main/lifecycle/index.ts
@@ -3,21 +3,19 @@ export * as ApplicationLifecycle from "./index"
 import { app, BrowserWindow } from "electron"
 import type { Event } from "electron"
 import { Context, Effect, Layer } from "effect"
-import { DeepLinksOpened } from "../../shared/ipc-rpc/events"
-import { emitIpcEvent } from "../ipc-events"
+import { DeepLinks } from "../deep-links"
 import { DesktopLogging, scoped } from "../native/logging"
 import { DesktopStorage } from "../storage"
 import { safeWebContentsURL } from "../windows/state"
-import { getLastFocusedWindow, getWindowByID, mainWindows, setAppQuitting, setRelaunchHandler } from "../windows"
+import { getLastFocusedWindow, mainWindows, setAppQuitting, setRelaunchHandler } from "../windows"
 import { marks } from "./marks"
 import { initializeFirstLaunchOnboarding } from "./onboarding"
 import { Shutdown } from "./shutdown"
-import { consoleReturnWindow } from "./deep-link"
 
 export interface Interface {
   readonly relaunch: () => void
   readonly prepareToRestart: Effect.Effect<void>
-  readonly consumeInitialDeepLinks: () => string[]
+  readonly deepLinks: DeepLinks.Interface
   readonly createWindow: () => BrowserWindow
   readonly restoreWindows: () => BrowserWindow[]
 }
@@ -32,7 +30,6 @@ const runtime = Layer.effect(
     const windows = yield* mainWindows()
     const createWindow = windows.create
     const restoreWindows = windows.restore
-    const pendingDeepLinks: string[] = []
     let shutdownReady = false
     let quitRequested = false
 
@@ -53,23 +50,7 @@ const runtime = Layer.effect(
       win.focus()
     }
 
-    const emitDeepLinks = (urls: string[]) => {
-      if (!urls.length) return
-      pendingDeepLinks.push(...urls)
-
-      const target = urls.flatMap((url) => {
-        const id = consoleReturnWindow(url)
-        const win = id ? getWindowByID(id) : null
-
-        return win ? [win] : []
-      })[0]
-
-      const win = target ?? getLastFocusedWindow()
-
-      if (win) emitIpcEvent(win.webContents, new DeepLinksOpened({ urls }))
-
-      return win
-    }
+    const deepLinks = yield* DeepLinks.make(focusWindow)
 
     const relaunch = () => {
       setAppQuitting()
@@ -90,7 +71,7 @@ const runtime = Layer.effect(
 
       if (urls.length) {
         runFork(Effect.logInfo("deep link received via second-instance", { urls }))
-        focusWindow(emitDeepLinks(urls) ?? null)
+        deepLinks.receive(urls)
       }
 
       if (!urls.length) focusWindow(getLastFocusedWindow())
@@ -99,7 +80,7 @@ const runtime = Layer.effect(
     const openUrl = (event: Event, url: string) => {
       event.preventDefault()
       runFork(Effect.logInfo("deep link received via open-url", { url }))
-      focusWindow(emitDeepLinks([url]) ?? null)
+      deepLinks.receive([url])
     }
 
     const beforeQuit = (event: Event) => {
@@ -179,7 +160,7 @@ const runtime = Layer.effect(
     return Service.of({
       relaunch,
       prepareToRestart,
-      consumeInitialDeepLinks: () => pendingDeepLinks.splice(0),
+      deepLinks,
       createWindow,
       restoreWindows: () => {
         if (!windowsWired) {
diff --git a/packages/desktop/src/main/windows/index.ts b/packages/desktop/src/main/windows/index.ts
index 892603f5a1c..bcb5298a1c9 100644
--- a/packages/desktop/src/main/windows/index.ts
+++ b/packages/desktop/src/main/windows/index.ts
@@ -45,7 +45,7 @@ const registry = createWindowRegistry<BrowserWindow>({
   write: (ids) => getStore().set(WINDOW_IDS_KEY, ids),
 })
 
-const opened = new Set<(win: BrowserWindow) => void>()
+const opened = new Set<(win: BrowserWindow, id: string) => void>()
 
 let relaunchHandler = () => {
   setAppQuitting()
@@ -99,13 +99,19 @@ export function getWindowByID(id: string) {
   return win
 }
 
+/** The persistent id of an app window, or undefined for popups and other native windows. */
+export function getWindowID(win: BrowserWindow) {
+  // An open window's id stays in the persisted list until it closes.
+  return registry.persisted().find((id) => registry.get(id) === win)
+}
+
 /** App windows that host the renderer, excluding popups and other native windows. */
 export function getMainWindows() {
   return registry.list().filter((win) => !win.isDestroyed())
 }
 
 /** Runs for each app window as it registers, before its renderer loads. */
-export function onMainWindow(listener: (win: BrowserWindow) => void) {
+export function onMainWindow(listener: (win: BrowserWindow, id: string) => void) {
   opened.add(listener)
 
   return () => {
@@ -234,7 +240,7 @@ export const mainWindows = Effect.fn("Window.make")(function* () {
         ),
       )
     })
-    opened.forEach((listener) => listener(win))
+    opened.forEach((listener) => listener(win, id))
   }
 
   return { create, restore }
diff --git a/packages/desktop/src/renderer/api-types.ts b/packages/desktop/src/renderer/api-types.ts
index d67385c1a44..1fad0d233a8 100644
--- a/packages/desktop/src/renderer/api-types.ts
+++ b/packages/desktop/src/renderer/api-types.ts
@@ -15,7 +15,8 @@ import type {
 export type ElectronAPI = {
   awaitInitialization(): Promise<ServerReadyData>
   reconnectService(): Promise<ServerReadyData>
-  consumeInitialDeepLinks(): Promise<string[]>
+  readyDeepLinks(): void
+  acknowledgeDeepLinks(attempt: number): void
   isFirstLaunchOnboardingPending(): Promise<boolean>
   finishFirstLaunchOnboarding(createDefaultProject: boolean): Promise<string | null>
   checkAppExists(appName: string): Promise<boolean>
@@ -35,7 +36,7 @@ export type ElectronAPI = {
   getWindowBootstrap(): WindowBootstrap
   themeReady(): Promise<void>
   onMenuCommand(cb: (id: string) => void): () => void
-  onDeepLink(cb: (urls: string[]) => void): () => void
+  onDeepLink(cb: (delivery: { attempt: number; urls: string[] }) => void): () => void
   openDirectoryPicker(opts?: DirectoryPickerOptions): Promise<string | string[] | null>
   openFilePicker(opts?: FilePickerOptions): Promise<PickedFiles | null>
   readPickedFile(token: string, path: string): Promise<ArrayBuffer>
diff --git a/packages/desktop/src/renderer/api.ts b/packages/desktop/src/renderer/api.ts
index f1e994456a2..4c9ef44e3dd 100644
--- a/packages/desktop/src/renderer/api.ts
+++ b/packages/desktop/src/renderer/api.ts
@@ -23,7 +23,8 @@ const seeded = window.electron.storageSnapshot.then((snapshot) => new Map(Object
 export const api: ElectronAPI = {
   awaitInitialization: () => invoke("AppAwaitInitialization"),
   reconnectService: () => invoke("AppReconnectService"),
-  consumeInitialDeepLinks: () => invoke("AppConsumeInitialDeepLinks").then(mutable),
+  readyDeepLinks: () => send("AppReadyDeepLinks"),
+  acknowledgeDeepLinks: (attempt) => send("AppAcknowledgeDeepLinks", { attempt }),
   isFirstLaunchOnboardingPending: () => invoke("AppIsFirstLaunchOnboardingPending"),
   finishFirstLaunchOnboarding: (createDefaultProject) =>
     invoke("AppFinishFirstLaunchOnboarding", { createDefaultProject }),
@@ -54,7 +55,7 @@ export const api: ElectronAPI = {
   getWindowBootstrap: () => window.electron.bootstrap,
   themeReady: () => invoke("WindowThemeReady"),
   onMenuCommand: (cb) => listen("MenuCommandTriggered", (event) => cb(event.id)),
-  onDeepLink: (cb) => listen("DeepLinksOpened", (event) => cb(mutable(event.urls))),
+  onDeepLink: (cb) => listen("DeepLinksOpened", (event) => cb({ attempt: event.attempt, urls: mutable(event.urls) })),
 
   openDirectoryPicker: (opts) => invoke("FilesOpenDirectoryPicker", { options: opts }).then(mutable),
   openFilePicker: (opts) => invoke("FilesOpenFilePicker", { options: opts }).then(mutable),
diff --git a/packages/desktop/src/renderer/startup/deep-links.ts b/packages/desktop/src/renderer/startup/deep-links.ts
index fff01a8413f..b056bbd18d6 100644
--- a/packages/desktop/src/renderer/startup/deep-links.ts
+++ b/packages/desktop/src/renderer/startup/deep-links.ts
@@ -2,9 +2,14 @@ import type { ElectronAPI } from "../api-types"
 
 const deepLinkEvent = "opencode:deep-link"
 
+// Main sends each link to one renderer at a time and forgets it once acknowledged, so a reload or a new window
+// never handles it again.
 export function startDeepLinks(api: ElectronAPI) {
-  void api.consumeInitialDeepLinks().then(emitDeepLinks)
-  api.onDeepLink(emitDeepLinks)
+  api.onDeepLink((delivery) => {
+    emitDeepLinks(delivery.urls)
+    api.acknowledgeDeepLinks(delivery.attempt)
+  })
+  api.readyDeepLinks()
 }
 
 function emitDeepLinks(urls: string[]) {
diff --git a/packages/desktop/src/shared/ipc-rpc/app.ts b/packages/desktop/src/shared/ipc-rpc/app.ts
index 9f3802806c3..1ddefa3c265 100644
--- a/packages/desktop/src/shared/ipc-rpc/app.ts
+++ b/packages/desktop/src/shared/ipc-rpc/app.ts
@@ -9,8 +9,11 @@ export const AppAwaitInitialization = Rpc.make("AppAwaitInitialization", { succe
 
 export const AppReconnectService = Rpc.make("AppReconnectService", { success: ServerReadyData })
 
-export const AppConsumeInitialDeepLinks = Rpc.make("AppConsumeInitialDeepLinks", {
-  success: Schema.Array(Schema.String),
+// The renderer listens for DeepLinksOpened before it reports ready, and acknowledges each delivery once handled.
+export const AppReadyDeepLinks = Rpc.make("AppReadyDeepLinks")
+
+export const AppAcknowledgeDeepLinks = Rpc.make("AppAcknowledgeDeepLinks", {
+  payload: { attempt: Schema.Number },
 })
 
 export const AppIsFirstLaunchOnboardingPending = Rpc.make("AppIsFirstLaunchOnboardingPending", {
@@ -69,7 +72,8 @@ export const AppRelaunch = Rpc.make("AppRelaunch")
 export const AppRpcs = RpcGroup.make(
   AppAwaitInitialization,
   AppReconnectService,
-  AppConsumeInitialDeepLinks,
+  AppReadyDeepLinks,
+  AppAcknowledgeDeepLinks,
   AppIsFirstLaunchOnboardingPending,
   AppFinishFirstLaunchOnboarding,
   AppCheckAppExists,
diff --git a/packages/desktop/src/shared/ipc-rpc/events.ts b/packages/desktop/src/shared/ipc-rpc/events.ts
index 584b3dde5b0..e90bc1044ac 100644
--- a/packages/desktop/src/shared/ipc-rpc/events.ts
+++ b/packages/desktop/src/shared/ipc-rpc/events.ts
@@ -4,6 +4,7 @@ import { Rpc, RpcGroup } from "effect/rpc"
 import { PluginInstalled, PluginMenubarItem, PluginPayload, PluginGuis } from "./plugins"
 
 export class DeepLinksOpened extends Schema.TaggedClass<DeepLinksOpened>()("DeepLinksOpened", {
+  attempt: Schema.Number,
   urls: Schema.Array(Schema.String),
 }) {}