diff --git a/apps/desktop/src/composables/__tests__/useTheme.spec.ts b/apps/desktop/src/composables/__tests__/useTheme.spec.ts
new file mode 100644
index 000000000..405af6816
--- /dev/null
+++ b/apps/desktop/src/composables/__tests__/useTheme.spec.ts
@@ -0,0 +1,110 @@
+// @vitest-environment happy-dom
+import { afterEach, beforeEach, describe, expect, it, vi } from "vitest";
+
+let mediaQueryChangeListener: ((event: MediaQueryListEvent) => void) | undefined;
+let mediaQueryMatches = false;
+const requestAnimationFrameMock = vi.fn((callback: FrameRequestCallback) => {
+  callback(0);
+  return 0;
+});
+const setTheme = vi.fn(async () => {});
+
+function installLocalStorageStub() {
+  const store = new Map<string, string>();
+  const storage = {
+    get length() {
+      return store.size;
+    },
+    clear: vi.fn(() => store.clear()),
+    getItem: vi.fn((key: string) => store.get(key) ?? null),
+    key: vi.fn((index: number) => [...store.keys()][index] ?? null),
+    removeItem: vi.fn((key: string) => store.delete(key)),
+    setItem: vi.fn((key: string, value: string) => store.set(key, String(value))),
+  } as Storage;
+  Object.defineProperty(globalThis, "localStorage", { configurable: true, value: storage });
+  Object.defineProperty(window, "localStorage", { configurable: true, value: storage });
+}
+
+function installBrowserStubs() {
+  const mediaQuery = {
+    get matches() {
+      return mediaQueryMatches;
+    },
+    addEventListener: vi.fn((event: string, listener: (event: MediaQueryListEvent) => void) => {
+      if (event === "change") mediaQueryChangeListener = listener;
+    }),
+    removeEventListener: vi.fn(),
+  };
+  vi.stubGlobal("navigator", { userAgent: "Mozilla/5.0 (X11; Linux x86_64)" });
+  vi.stubGlobal("requestAnimationFrame", requestAnimationFrameMock);
+  Object.defineProperty(window, "matchMedia", { configurable: true, value: vi.fn(() => mediaQuery) });
+}
+
+async function loadTheme(mode: "light" | "dark" | "system" = "system") {
+  window.localStorage.setItem("dbx-theme", mode);
+  const { useTheme } = await import("@/composables/useTheme");
+  return useTheme();
+}
+
+async function flushDynamicImport() {
+  await Promise.resolve();
+  await new Promise((resolve) => setTimeout(resolve, 0));
+}
+
+describe("useTheme on Linux", () => {
+  beforeEach(() => {
+    vi.resetModules();
+    vi.clearAllMocks();
+    vi.unstubAllGlobals();
+    installLocalStorageStub();
+    window.localStorage.clear();
+    document.documentElement.className = "";
+    document.documentElement.style.colorScheme = "";
+    mediaQueryChangeListener = undefined;
+    mediaQueryMatches = false;
+    installBrowserStubs();
+    vi.doMock("@/lib/backend/tauriRuntime", () => ({ isTauriRuntime: () => true }));
+    vi.doMock("@tauri-apps/api/window", () => ({ getCurrentWindow: () => ({ setTheme }) }));
+  });
+
+  afterEach(() => {
+    vi.doUnmock("@/lib/backend/tauriRuntime");
+    vi.doUnmock("@tauri-apps/api/window");
+    vi.unstubAllGlobals();
+  });
+
+  it("uses the Linux system preference after a fresh startup without overwriting GTK", async () => {
+    mediaQueryMatches = true;
+    const theme = await loadTheme();
+
+    theme.applyTheme();
+
+    expect(theme.isDark.value).toBe(true);
+    expect(document.documentElement.classList.contains("dark")).toBe(true);
+    expect(setTheme).not.toHaveBeenCalled();
+  });
+
+  it("continues to apply system preference changes without writing the native theme", async () => {
+    const theme = await loadTheme();
+    theme.applyTheme();
+
+    mediaQueryChangeListener?.({ matches: true } as MediaQueryListEvent);
+
+    expect(theme.isDark.value).toBe(true);
+    expect(document.documentElement.classList.contains("dark")).toBe(true);
+    expect(setTheme).not.toHaveBeenCalled();
+  });
+
+  it("still writes explicit dark and light choices to the native Linux window theme", async () => {
+    const theme = await loadTheme("dark");
+    expect(theme.themeMode.value).toBe("dark");
+
+    theme.applyTheme();
+    await flushDynamicImport();
+    expect(setTheme).toHaveBeenLastCalledWith("dark");
+
+    theme.setThemeMode("light");
+    await flushDynamicImport();
+    expect(setTheme).toHaveBeenLastCalledWith("light");
+  });
+});
diff --git a/apps/desktop/src/composables/useTheme.ts b/apps/desktop/src/composables/useTheme.ts
index a17679466..7ee9093c6 100644
--- a/apps/desktop/src/composables/useTheme.ts
+++ b/apps/desktop/src/composables/useTheme.ts
@@ -18,6 +18,10 @@ import {
 import { safeLocalStorageGet, safeLocalStorageSet } from "@/lib/backend/safeStorage";
 import { isTauriRuntime } from "@/lib/backend/tauriRuntime";
 
+function isLinuxTauriRuntime() {
+  return isTauriRuntime() && typeof navigator !== "undefined" && /linux/i.test(navigator.userAgent);
+}
+
 const savedThemeMode = safeLocalStorageGet(APP_THEME_STORAGE_KEY);
 const themeMode = ref<AppThemeMode>(normalizeAppThemeMode(savedThemeMode));
 const savedThemePalette = safeLocalStorageGet(APP_THEME_PALETTE_STORAGE_KEY);
@@ -67,19 +71,24 @@ function applyTheme() {
   // force reflow so the class toggle takes effect before re-enabling transitions
   doc.offsetHeight; // eslint-disable-line @typescript-eslint/no-unused-expressions
   requestAnimationFrame(() => doc.classList.remove("disable-transitions"));
-
   if (!isTauriRuntime()) return;
+
+  const tauriTheme = getTauriThemeForMode(themeMode.value);
+  // Tauri owns the Linux GTK preference. Calling setTheme(null) here forces it
+  // to light, so only skip the native system-theme write and keep explicit modes.
+  if (isLinuxTauriRuntime() && tauriTheme == null) return;
+
   if (cachedTauriWindow) {
     cachedTauriWindow
       .getCurrentWindow()
-      .setTheme(getTauriThemeForMode(themeMode.value))
+      .setTheme(tauriTheme)
       .catch(() => {});
   } else {
     import("@tauri-apps/api/window").then((mod) => {
       cachedTauriWindow = mod;
       mod
         .getCurrentWindow()
-        .setTheme(getTauriThemeForMode(themeMode.value))
+        .setTheme(tauriTheme)
         .catch(() => {});
     });
   }