diff --git a/Cargo.lock b/Cargo.lock
index 3340244a3..791544fe5 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -7531,6 +7531,23 @@ dependencies = [
  "zbus",
 ]
 
+[[package]]
+name = "tauri-plugin-single-instance"
+version = "2.4.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "db817fe9295e19b7d8357e900af31edb93703dd9fb6de524b007b47b6afc63b0"
+dependencies = [
+ "serde",
+ "serde_json",
+ "tauri",
+ "tauri-plugin-deep-link",
+ "thiserror 2.0.20",
+ "tokio",
+ "tracing",
+ "windows-sys 0.60.2",
+ "zbus",
+]
+
 [[package]]
 name = "tauri-runtime"
 version = "2.11.3"
@@ -8180,6 +8197,7 @@ dependencies = [
  "tauri-plugin-keystore",
  "tauri-plugin-log",
  "tauri-plugin-opener",
+ "tauri-plugin-single-instance",
  "tauri-test",
  "tempfile",
  "tokio",
diff --git a/src-tauri/Cargo.toml b/src-tauri/Cargo.toml
index a8a878014..2f3c96ab7 100644
--- a/src-tauri/Cargo.toml
+++ b/src-tauri/Cargo.toml
@@ -31,6 +31,7 @@ libc = "0.2"
 tauri-plugin-cli = "2.4.1"
 # Parses CLI args before Tauri starts (see `cli::args`); same version the plugin uses.
 clap = "4"
+tauri-plugin-single-instance = { version = "2", features = ["deep-link"] }
 
 [dependencies]
 tauri = { version = "2.10.3", features = ["protocol-asset", "unstable"] }
diff --git a/src-tauri/src/lib.rs b/src-tauri/src/lib.rs
index ca6860118..bf2234524 100644
--- a/src-tauri/src/lib.rs
+++ b/src-tauri/src/lib.rs
@@ -148,6 +148,47 @@ pub fn emit_to_focused<S: serde::Serialize + Clone>(app: &AppHandle, event: &str
   let _ = app.emit_to(EventTarget::webview_window(&label), event, payload);
 }
 
+/// What a `treq://` deep link asks the app to do.
+#[cfg(desktop)]
+#[derive(Debug, PartialEq, Eq)]
+enum DeepLinkKind {
+  /// `treq://agent/start?...`: start an agent in the window open on a repo.
+  Agent,
+  /// `treq://auth/callback?token=...`: finish browser sign-in.
+  AuthCallback,
+  Unknown,
+}
+
+/// Sorts a deep link by what it asks for. An auth callback is matched by the
+/// same rule as `authCallbackToken` in `src/lib/auth-deep-link.ts`.
+#[cfg(desktop)]
+fn classify_deep_link(url: &str) -> DeepLinkKind {
+  if url.starts_with("treq://agent/start?") {
+    return DeepLinkKind::Agent;
+  }
+  match url::Url::parse(url) {
+    Ok(parsed)
+      if parsed.scheme() == "treq"
+        && parsed.host_str() == Some("auth")
+        && parsed.path() == "/callback" =>
+    {
+      DeepLinkKind::AuthCallback
+    }
+    _ => DeepLinkKind::Unknown,
+  }
+}
+
+/// Brings the window a menu event would target to the front.
+#[cfg(desktop)]
+fn focus_target_window(app: &AppHandle) {
+  let Some(window) = resolve_menu_target_label(app).and_then(|l| app.get_webview_window(&l)) else {
+    return;
+  };
+  let _ = window.unminimize();
+  let _ = window.show();
+  let _ = window.set_focus();
+}
+
 /// Handles the regular "Open..." menu action (CmdOrCtrl+O).
 ///
 /// Guarded the same way as "Open in New Window": a macOS File-menu
@@ -298,8 +339,17 @@ pub fn run() {
   if is_cli_process(std::env::args_os()) {
     std::process::exit(cli::args::run(std::env::args_os()));
   }
+  let builder = tauri::Builder::default();
+  // Must be the first plugin. On Windows and Linux a `treq://` link starts a
+  // second process; this plugin makes it exit and hands its arguments to the
+  // running app. The `deep-link` feature passes the link on to `on_open_url`
+  // below, so the callback only brings the app to the front.
+  #[cfg(desktop)]
+  let builder = builder.plugin(tauri_plugin_single_instance::init(|app, _args, _cwd| {
+    focus_target_window(app);
+  }));
   let builder = {
-    let builder = tauri::Builder::default()
+    let builder = builder
       .plugin(
         tauri_plugin_log::Builder::new()
           .level(tauri_plugin_log::log::LevelFilter::Info)
@@ -439,21 +489,36 @@ pub fn run() {
       #[cfg(desktop)]
       {
         use tauri_plugin_deep_link::DeepLinkExt;
+        // Installers register `treq://` with the OS. An AppImage or a dev
+        // build is not installed, so it registers itself at startup.
+        #[cfg(any(target_os = "linux", all(debug_assertions, windows)))]
+        if let Err(err) = app.deep_link().register_all() {
+          log::warn!("failed to register deep link schemes: {err}");
+        }
         let handle = app.handle().clone();
         app.deep_link().on_open_url(move |event| {
           let urls: Vec<String> = event.urls().into_iter().map(|u| u.to_string()).collect();
           for url in urls {
-            if let Some(request) = parse_agent_request_from_url(&url) {
-              let response = route_agent_dispatch_request(&handle, &request);
-              if response.status != "handled" {
-                log::info!(
-                  "agent deep link unmatched repo={} request_id={}",
-                  request.repo,
-                  request.request_id
-                );
+            match classify_deep_link(&url) {
+              // One window only: the sign-in token can be exchanged once.
+              DeepLinkKind::AuthCallback => {
+                emit_to_focused(&handle, "deep-link-received", vec![url]);
               }
-            } else if !route_agent_deep_link(&handle, url) {
-              log::info!("agent deep link ignored (no matching window/repo)");
+              DeepLinkKind::Agent => {
+                if let Some(request) = parse_agent_request_from_url(&url) {
+                  let response = route_agent_dispatch_request(&handle, &request);
+                  if response.status != "handled" {
+                    log::info!(
+                      "agent deep link unmatched repo={} request_id={}",
+                      request.repo,
+                      request.request_id
+                    );
+                  }
+                } else if !route_agent_deep_link(&handle, url) {
+                  log::info!("agent deep link ignored (no matching window/repo)");
+                }
+              }
+              DeepLinkKind::Unknown => log::info!("deep link ignored (unrecognized url)"),
             }
           }
         });
@@ -1002,6 +1067,38 @@ mod tests {
     assert_eq!(extract_repo_from_agent_deep_link(url), None);
   }
 
+  #[test]
+  fn classifies_agent_start_link_as_agent() {
+    let url = "treq://agent/start?repo=%2Ftmp%2Frepo&request_id=req-1";
+    assert_eq!(super::classify_deep_link(url), super::DeepLinkKind::Agent);
+  }
+
+  #[test]
+  fn classifies_auth_callback_link_as_auth_callback() {
+    let url = "treq://auth/callback?token=abc";
+    assert_eq!(
+      super::classify_deep_link(url),
+      super::DeepLinkKind::AuthCallback
+    );
+  }
+
+  #[test]
+  fn classifies_other_links_as_unknown() {
+    for url in [
+      "treq://auth/other?token=abc",
+      "treq://auth/callback/extra?token=abc",
+      "https://treq.dev/auth/callback?token=abc",
+      "treq://settings",
+      "not a url",
+    ] {
+      assert_eq!(
+        super::classify_deep_link(url),
+        super::DeepLinkKind::Unknown,
+        "{url}"
+      );
+    }
+  }
+
   #[test]
   fn parse_agent_request_from_url_round_trips() {
     let request = crate::agent_dispatch::AgentDispatchRequest {
diff --git a/src/stores/AppStoreEffects.test.tsx b/src/stores/AppStoreEffects.test.tsx
new file mode 100644
index 000000000..3e7f6f839
--- /dev/null
+++ b/src/stores/AppStoreEffects.test.tsx
@@ -0,0 +1,55 @@
+import { render, waitFor } from "@testing-library/react";
+import { listen } from "@tauri-apps/api/event";
+import { afterEach, beforeEach, describe, expect, it, vi } from "vitest";
+import { AppStoreEffects } from "./AppStoreEffects";
+import { useAuthStore } from "./authStore";
+
+type DeepLinkHandler = (event: { payload: string[] }) => Promise<void>;
+
+// The desktop backend emits `deep-link-received` with `vec![url]`.
+async function renderAndGetDeepLinkHandler(): Promise<DeepLinkHandler> {
+  render(<AppStoreEffects />);
+  await waitFor(() =>
+    expect(listen).toHaveBeenCalledWith(
+      "deep-link-received",
+      expect.any(Function),
+    ),
+  );
+  const calls = vi
+    .mocked(listen)
+    .mock.calls.filter(([event]) => event === "deep-link-received");
+  expect(calls).toHaveLength(1);
+  return calls[0][1] as unknown as DeepLinkHandler;
+}
+
+describe("AppStoreEffects deep links", () => {
+  const originalExchangeToken = useAuthStore.getState().exchangeToken;
+  const exchangeToken = vi.fn().mockResolvedValue(undefined);
+
+  beforeEach(() => {
+    vi.mocked(listen).mockClear();
+    exchangeToken.mockClear();
+    useAuthStore.setState({ exchangeToken });
+  });
+
+  afterEach(() => {
+    useAuthStore.setState({ exchangeToken: originalExchangeToken });
+  });
+
+  it("exchanges the token from an auth callback once", async () => {
+    const onDeepLink = await renderAndGetDeepLinkHandler();
+
+    await onDeepLink({ payload: ["treq://auth/callback?token=abc"] });
+
+    expect(exchangeToken).toHaveBeenCalledOnce();
+    expect(exchangeToken).toHaveBeenCalledWith("abc");
+  });
+
+  it("does not exchange anything for an agent deep link", async () => {
+    const onDeepLink = await renderAndGetDeepLinkHandler();
+
+    await onDeepLink({ payload: ["treq://agent/start?repo=%2Ftmp%2Frepo"] });
+
+    expect(exchangeToken).not.toHaveBeenCalled();
+  });
+});