diff --git a/packages/desktop/src/main/index.ts b/packages/desktop/src/main/index.ts
index c7c1643092d1..bdd436649aad 100644
--- a/packages/desktop/src/main/index.ts
+++ b/packages/desktop/src/main/index.ts
@@ -48,6 +48,7 @@ import { registerWslIpcHandlers } from "./wsl/ipc"
 import { spawnWslSidecar } from "./wsl/sidecar"
 import { migrate } from "./migrate"
 import { cleanupStoreFiles } from "./store-cleanup"
+import { flushAllStores } from "./store"
 
 const APP_NAMES: Record<string, string> = {
   dev: "OpenCode Dev",
@@ -221,11 +222,13 @@ const main = Effect.gen(function* () {
 
   app.on("before-quit", () => {
     setAppQuitting()
+    flushAllStores()
     void stopSidecars()
   })
 
   app.on("will-quit", () => {
     setAppQuitting()
+    flushAllStores()
     void stopSidecars()
   })
 
diff --git a/packages/desktop/src/main/store.test.ts b/packages/desktop/src/main/store.test.ts
new file mode 100644
index 000000000000..6efd25cc865a
--- /dev/null
+++ b/packages/desktop/src/main/store.test.ts
@@ -0,0 +1,58 @@
+import { describe, expect, test, beforeEach, afterEach, vi } from "bun:test"
+import { BufferedStore } from "./store"
+
+class MemoryStore {
+  public data = new Map<string, unknown>()
+  get(key: string) {
+    return this.data.get(key)
+  }
+  set(key: string, value: unknown) {
+    this.data.set(key, value)
+  }
+  delete(key: string) {
+    this.data.delete(key)
+  }
+}
+
+describe("BufferedStore", () => {
+  test("returns pending value before flush", () => {
+    const underlying = new MemoryStore()
+    const store = new BufferedStore(underlying as any, 100)
+
+    store.set("theme", "dark")
+
+    // MemoryStore hasn't been updated yet before flush
+    expect(underlying.data.get("theme")).toBeUndefined()
+
+    // But BufferedStore returns the pending write immediately
+    expect(store.get("theme")).toBe("dark")
+  })
+
+  test("flushes pending writes to underlying store on flush()", () => {
+    const underlying = new MemoryStore()
+    const store = new BufferedStore(underlying as any, 100)
+
+    store.set("key1", "value1")
+    store.set("key2", "value2")
+    store.flush()
+
+    expect(underlying.data.get("key1")).toBe("value1")
+    expect(underlying.data.get("key2")).toBe("value2")
+  })
+
+  test("buffers delete operations until flush()", () => {
+    const underlying = new MemoryStore()
+    underlying.set("key1", "value1")
+
+    const store = new BufferedStore(underlying as any, 100)
+    store.delete("key1")
+
+    // Still in underlying before flush
+    expect(underlying.data.get("key1")).toBe("value1")
+    // Buffered as deleted
+    expect(store.get("key1")).toBeUndefined()
+
+    store.flush()
+    expect(underlying.data.has("key1")).toBe(false)
+  })
+})
diff --git a/packages/desktop/src/main/store.ts b/packages/desktop/src/main/store.ts
index 687429ed4365..c955d7039894 100644
--- a/packages/desktop/src/main/store.ts
+++ b/packages/desktop/src/main/store.ts
@@ -6,30 +6,124 @@ import { join } from "node:path"
 import { SETTINGS_STORE } from "./store-keys"
 import { deleteStoreFileIfEmpty } from "./store-cleanup"
 
-const cache = new Map<string, Store>()
+const DELETED = Symbol("DELETED")
 
-// We cannot instantiate the electron-store at module load time because
-// module import hoisting causes this to run before app.setPath("userData", ...)
-// in index.ts has executed, which would result in files being written to the default directory
-// (e.g. bad: %APPDATA%\@opencode-ai\desktop\opencode.settings vs good: %APPDATA%\ai.opencode.desktop.dev\opencode.settings).
-export function getStore(name = SETTINGS_STORE) {
+export class BufferedStore {
+  private pending = new Map<string, unknown>()
+  private cleared = false
+  private timer: ReturnType<typeof setTimeout> | null = null
+
+  constructor(
+    private target: {
+      get(key: string): unknown
+      set(key: string, val: unknown): void
+      delete(key: string): void
+      clear(): void
+      has(key: string): boolean
+      store: Record<string, unknown>
+    },
+    private delay = 150,
+  ) {}
+
+  get store(): Record<string, unknown> {
+    const base = this.cleared ? {} : { ...this.target.store }
+    for (const [key, value] of this.pending) {
+      if (value === DELETED) {
+        delete base[key]
+      } else {
+        base[key] = value
+      }
+    }
+    return base
+  }
+
+  has(key: string): boolean {
+    if (this.pending.has(key)) {
+      return this.pending.get(key) !== DELETED
+    }
+    if (this.cleared) return false
+    return this.target.has(key)
+  }
+
+  get(key: string) {
+    if (this.pending.has(key)) {
+      const val = this.pending.get(key)
+      return val === DELETED ? undefined : val
+    }
+    if (this.cleared) return undefined
+    return this.target.get(key)
+  }
+
+  set(key: string, value: unknown) {
+    this.pending.set(key, value)
+    this.scheduleFlush()
+  }
+
+  delete(key: string) {
+    this.pending.set(key, DELETED)
+    this.scheduleFlush()
+  }
+
+  clear() {
+    this.cleared = true
+    this.pending.clear()
+    this.scheduleFlush()
+  }
+
+  flush() {
+    if (this.timer) {
+      clearTimeout(this.timer)
+      this.timer = null
+    }
+    if (this.cleared) {
+      this.target.clear()
+      this.cleared = false
+    }
+    for (const [key, value] of this.pending) {
+      if (value === DELETED) {
+        this.target.delete(key)
+      } else {
+        this.target.set(key, value)
+      }
+    }
+    this.pending.clear()
+  }
+
+  private scheduleFlush() {
+    if (this.timer) return
+    this.timer = setTimeout(() => this.flush(), this.delay)
+  }
+}
+
+const cache = new Map<string, BufferedStore>()
+
+export function getStore(name = SETTINGS_STORE): BufferedStore {
   const cached = cache.get(name)
   if (cached) return cached
-  const next = new Store({
+  const underlying = new Store({
     name,
     cwd: electron.app.getPath("userData"),
     fileExtension: "",
     accessPropertiesByDotNotation: false,
   })
+  const next = new BufferedStore(underlying)
   cache.set(name, next)
   return next
 }
 
+export function flushAllStores() {
+  for (const store of cache.values()) {
+    store.flush()
+  }
+}
+
 export async function removeStoreFileIfEmpty(name: string) {
+  cache.get(name)?.flush()
   if (await deleteStoreFileIfEmpty(electron.app.getPath("userData"), name)) cache.delete(name)
 }
 
 export function removeStoreFile(name: string) {
+  cache.get(name)?.flush()
   rmSync(join(electron.app.getPath("userData"), name), { force: true })
   cache.delete(name)
 }