diff --git a/packages/opencode/src/config/config.ts b/packages/opencode/src/config/config.ts
index 1c99a45b17..f1e9b6a3e5 100644
--- a/packages/opencode/src/config/config.ts
+++ b/packages/opencode/src/config/config.ts
@@ -322,10 +322,7 @@ function patchJsonc(input: string, patch: unknown, path: string[] = []): string
     return applyEdits(input, edits)
   }
 
-  return Object.entries(patch).reduce((result, [key, value]) => {
-    if (value === undefined) return result
-    return patchJsonc(result, value, [...path, key])
-  }, input)
+  return Object.entries(patch).reduce((result, [key, value]) => patchJsonc(result, value, [...path, key]), input)
 }
 
 function writable(info: Info) {
@@ -333,6 +330,13 @@ function writable(info: Info) {
   return next
 }
 
+function writableGlobal(info: Info) {
+  const next = writable(info)
+  // When a user changes config from a value back to default in the Desktop app, we dont want to leave a blank `"shell": "",` key
+  if ("shell" in next && next.shell === "") return { ...next, shell: undefined }
+  return next
+}
+
 export const ConfigDirectoryTypoError = NamedError.create(
   "ConfigDirectoryTypoError",
   z.object({
@@ -761,15 +765,16 @@ export const layer = Layer.effect(
     const updateGlobal = Effect.fn("Config.updateGlobal")(function* (config: Info) {
       const file = globalConfigFile()
       const before = (yield* readConfigFile(file)) ?? "{}"
+      const patch = writableGlobal(config)
 
       let next: Info
       if (!file.endsWith(".jsonc")) {
         const existing = ConfigParse.schema(Info.zod, ConfigParse.jsonc(before, file), file)
-        const merged = mergeDeep(writable(existing), writable(config))
+        const merged = mergeDeep(writable(existing), patch)
         yield* fs.writeFileString(file, JSON.stringify(merged, null, 2)).pipe(Effect.orDie)
         next = merged
       } else {
-        const updated = patchJsonc(before, writable(config))
+        const updated = patchJsonc(before, patch)
         next = ConfigParse.schema(Info.zod, ConfigParse.jsonc(updated, file), file)
         yield* fs.writeFileString(file, updated).pipe(Effect.orDie)
       }
diff --git a/packages/opencode/test/config/config.test.ts b/packages/opencode/test/config/config.test.ts
index 815919ee20..65e95c0bd5 100644
--- a/packages/opencode/test/config/config.test.ts
+++ b/packages/opencode/test/config/config.test.ts
@@ -55,6 +55,8 @@ const it = testEffect(layer)
 const load = () => Effect.runPromise(Config.Service.use((svc) => svc.get()).pipe(Effect.scoped, Effect.provide(layer)))
 const save = (config: Config.Info) =>
   Effect.runPromise(Config.Service.use((svc) => svc.update(config)).pipe(Effect.scoped, Effect.provide(layer)))
+const saveGlobal = (config: Config.Info) =>
+  Effect.runPromise(Config.Service.use((svc) => svc.updateGlobal(config)).pipe(Effect.scoped, Effect.provide(layer)))
 const clear = (wait = false) =>
   Effect.runPromise(Config.Service.use((svc) => svc.invalidate(wait)).pipe(Effect.scoped, Effect.provide(layer)))
 const listDirs = () =>
@@ -180,6 +182,64 @@ test("updates config and preserves empty shell sentinel", async () => {
   })
 })
 
+test("updates global config and omits empty shell key in json", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      await writeConfig(dir, {
+        $schema: "https://opencode.ai/config.json",
+        shell: "bash",
+      })
+    },
+  })
+
+  const prev = Global.Path.config
+  ;(Global.Path as { config: string }).config = tmp.path
+  await clear(true)
+
+  try {
+    await saveGlobal({ shell: "" } as any)
+
+    const writtenConfig = await Filesystem.readJson<{ shell?: string }>(path.join(tmp.path, "opencode.json"))
+    expect("shell" in writtenConfig).toBe(false)
+  } finally {
+    ;(Global.Path as { config: string }).config = prev
+    await clear(true)
+  }
+})
+
+test("updates global config and omits empty shell key in jsonc", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      await Filesystem.write(
+        path.join(dir, "opencode.jsonc"),
+        JSON.stringify({
+          $schema: "https://opencode.ai/config.json",
+          shell: "bash",
+          model: "test/model",
+        }),
+      )
+    },
+  })
+
+  const prev = Global.Path.config
+  ;(Global.Path as { config: string }).config = tmp.path
+  await clear(true)
+
+  try {
+    await saveGlobal({ shell: "" } as any)
+
+    const file = path.join(tmp.path, "opencode.jsonc")
+    const writtenConfig = await Filesystem.readText(file)
+    const parsed = ConfigParse.schema(Config.Info.zod, ConfigParse.jsonc(writtenConfig, file), file)
+    expect(writtenConfig).not.toContain('"shell"')
+    expect(parsed.shell).toBeUndefined()
+    expect(parsed.model).toBe("test/model")
+  } finally {
+    ;(Global.Path as { config: string }).config = prev
+    await clear(true)
+  }
+})
+
 test("loads formatter boolean config", async () => {
   await using tmp = await tmpdir({
     init: async (dir) => {