diff --git a/packages/core/src/filesystem.ts b/packages/core/src/filesystem.ts
index 8a1cc3a08fc3..0a9e3b783fd4 100644
--- a/packages/core/src/filesystem.ts
+++ b/packages/core/src/filesystem.ts
@@ -1,6 +1,7 @@
 import { NodeFileSystem } from "@effect/platform-node"
 import { dirname, join, relative, resolve as pathResolve } from "path"
 import { realpathSync } from "fs"
+import { randomUUID } from "crypto"
 import * as NFS from "fs/promises"
 import { lookup } from "mime-types"
 import { Effect, FileSystem, Layer, Schema, Context } from "effect"
@@ -84,12 +85,6 @@ export namespace AppFileSystem {
         return JSON.parse(text)
       })
 
-      const writeJson = Effect.fn("FileSystem.writeJson")(function* (path: string, data: unknown, mode?: number) {
-        const content = JSON.stringify(data, null, 2)
-        yield* fs.writeFileString(path, content)
-        if (mode) yield* fs.chmod(path, mode)
-      })
-
       const ensureDir = Effect.fn("FileSystem.ensureDir")(function* (path: string) {
         yield* fs.makeDirectory(path, { recursive: true })
       })
@@ -99,19 +94,25 @@ export namespace AppFileSystem {
         content: string | Uint8Array,
         mode?: number,
       ) {
-        const write = typeof content === "string" ? fs.writeFileString(path, content) : fs.writeFile(path, content)
-
-        yield* write.pipe(
-          Effect.catchIf(
-            (e) => e.reason._tag === "NotFound",
-            () =>
-              Effect.gen(function* () {
-                yield* fs.makeDirectory(dirname(path), { recursive: true })
-                yield* write
-              }),
-          ),
-        )
-        if (mode) yield* fs.chmod(path, mode)
+        yield* Effect.tryPromise({
+          try: async () => {
+            await NFS.mkdir(dirname(path), { recursive: true })
+            const tmp = path + "." + process.pid + "." + randomUUID() + ".tmp"
+            try {
+              await NFS.writeFile(tmp, content, mode ? { mode } : undefined)
+              if (mode) await NFS.chmod(tmp, mode)
+              await NFS.rename(tmp, path)
+            } catch (e) {
+              await NFS.rm(tmp, { force: true }).catch(() => {})
+              throw e
+            }
+          },
+          catch: (cause) => new FileSystemError({ method: "writeWithDirs", cause }),
+        })
+      })
+
+      const writeJson = Effect.fn("FileSystem.writeJson")(function* (path: string, data: unknown, mode?: number) {
+        yield* writeWithDirs(path, JSON.stringify(data, null, 2), mode)
       })
 
       const glob = Effect.fn("FileSystem.glob")(function* (pattern: string, options?: Glob.Options) {
diff --git a/packages/opencode/test/filesystem/filesystem.test.ts b/packages/opencode/test/filesystem/filesystem.test.ts
index 2d9271e873eb..b297dbd8255b 100644
--- a/packages/opencode/test/filesystem/filesystem.test.ts
+++ b/packages/opencode/test/filesystem/filesystem.test.ts
@@ -76,6 +76,21 @@ describe("AppFileSystem", () => {
         expect(result).toEqual(data)
       }),
     )
+
+    it(
+      "writes JSON through a complete replacement file",
+      Effect.gen(function* () {
+        const fs = yield* AppFileSystem.Service
+        const tmp = yield* fs.makeTempDirectoryScoped()
+        const file = path.join(tmp, "nested", "data.json")
+
+        yield* fs.writeJson(file, { value: "old" })
+        yield* fs.writeJson(file, { value: "new" })
+
+        expect(yield* fs.readJson(file)).toEqual({ value: "new" })
+        expect(yield* fs.glob("*.tmp", { cwd: path.dirname(file) })).toEqual([])
+      }),
+    )
   })
 
   describe("ensureDir", () => {