diff --git a/packages/core/src/config/normalize.ts b/packages/core/src/config/normalize.ts
index c6c58a65b9f..f858b71c817 100644
--- a/packages/core/src/config/normalize.ts
+++ b/packages/core/src/config/normalize.ts
@@ -130,7 +130,8 @@ export function normalize(input: unknown): Result {
 
   const legacyAgents = mapValues(
     decodeMap(input.agent, ConfigAgentV1.Info, ["agent"], diagnostics, decodeValue),
-    (value) => canonical(ConfigAgent.Info, ConfigMigrateV1.migrateAgent(value)),
+    (value, name) =>
+      canonical(ConfigAgent.Info, ConfigMigrateV1.migrateAgent(value, legacyPermission(input.agent, name))),
   )
   const legacySmallModel = own(input, "small_model")
     ? decodeValue(Schema.String, input.small_model, ["small_model"], diagnostics)
@@ -149,8 +150,13 @@ export function normalize(input: unknown): Result {
       model: migratedSmallModel,
       ...legacyAgents.title,
     }
-  const modeAgents = mapValues(decodeMap(input.mode, ConfigAgentV1.Info, ["mode"], diagnostics, decodeValue), (value) =>
-    canonical(ConfigAgent.Info, ConfigMigrateV1.migrateAgent({ ...value, mode: "primary" })),
+  const modeAgents = mapValues(
+    decodeMap(input.mode, ConfigAgentV1.Info, ["mode"], diagnostics, decodeValue),
+    (value, name) =>
+      canonical(
+        ConfigAgent.Info,
+        ConfigMigrateV1.migrateAgent({ ...value, mode: "primary" }, legacyPermission(input.mode, name)),
+      ),
   )
   const migratedAgents = mergeMaps(legacyAgents, modeAgents, ["agents"], diagnostics)
   const nativeAgents = decodeMap(input.agents, ConfigAgent.Info, ["agents"], diagnostics, decodeEncoded)
@@ -742,10 +748,10 @@ function mergeMaps(
   return result
 }
 
-function mapValues<A>(input: Readonly<Record<string, A>>, map: (value: A) => unknown) {
+function mapValues<A>(input: Readonly<Record<string, A>>, map: (value: A, key: string) => unknown) {
   return Object.fromEntries(
     Object.entries(input).flatMap(([key, value]) => {
-      const mapped = map(value)
+      const mapped = map(value, key)
       return mapped === undefined ? [] : [[key, mapped]]
     }),
   )
@@ -795,6 +801,10 @@ function isPlainRecord(value: unknown): value is Record<string, unknown> {
   return prototype === Object.prototype || prototype === null
 }
 
+function legacyPermission(agents: unknown, name: string) {
+  return isRecord(agents) && isRecord(agents[name]) ? agents[name].permission : undefined
+}
+
 function own(value: Record<string, unknown>, key: string) {
   return Object.hasOwn(value, key)
 }
diff --git a/packages/core/src/config/plugin/agent.ts b/packages/core/src/config/plugin/agent.ts
index 1d3949d015e..8bcfc726cdc 100644
--- a/packages/core/src/config/plugin/agent.ts
+++ b/packages/core/src/config/plugin/agent.ts
@@ -195,9 +195,8 @@ function decode(file: { directory: string; filepath: string; primary: boolean },
       : markdown.data
   const agent = legacy
     ? Option.getOrUndefined(
-        Option.map(
-          decodeLegacyAgent({ name, ...markdown.data, prompt: body }, { errors: "all" }),
-          ConfigMigrateV1.migrateAgent,
+        Option.map(decodeLegacyAgent({ name, ...markdown.data, prompt: body }, { errors: "all" }), (agent) =>
+          ConfigMigrateV1.migrateAgent(agent, markdown.data.permission),
         ),
       )
     : Option.getOrUndefined(decodeAgent({ ...data, system: body }, { errors: "all" }))
diff --git a/packages/core/src/v1/config/migrate.ts b/packages/core/src/v1/config/migrate.ts
index 28488aa5134..a30dbfff7d7 100644
--- a/packages/core/src/v1/config/migrate.ts
+++ b/packages/core/src/v1/config/migrate.ts
@@ -113,6 +113,12 @@ function permissions(info?: ConfigPermissionV1.Info, tools?: Readonly<Record<str
   return rules.length ? rules : undefined
 }
 
+// Effect emits declared keys in schema order. Permission rules are last-match-wins, so restore the author's key order.
+function inInputOrder(info: ConfigPermissionV1.Info | undefined, input: unknown): ConfigPermissionV1.Info | undefined {
+  if (info === undefined || typeof input !== "object" || input === null) return info
+  return Object.fromEntries(Object.keys(input).flatMap((key) => (Object.hasOwn(info, key) ? [[key, info[key]]] : [])))
+}
+
 // Map v1 permission/tool keys onto their renamed v2 tool actions so migrated rules keep matching.
 export function normalizeAction(action: string) {
   if (action === "write" || action === "patch") return "edit"
@@ -138,7 +144,7 @@ function agents(info: typeof ConfigV1.Info.Type) {
   }
 }
 
-export function migrateAgent(info: ConfigAgentV1.Info) {
+export function migrateAgent(info: ConfigAgentV1.Info, permission?: unknown) {
   const body = {
     ...info.options,
     ...(info.temperature === undefined ? {} : { temperature: info.temperature }),
@@ -156,7 +162,7 @@ export function migrateAgent(info: ConfigAgentV1.Info) {
         color: info.color === undefined ? undefined : info.color.startsWith("#") ? info.color : "#aaaaaa",
         steps: info.steps,
         disabled: info.disable,
-        permissions: permissions(info.permission),
+        permissions: permissions(inInputOrder(info.permission, permission)),
       }),
     ),
   )
diff --git a/packages/core/test/config/agent.test.ts b/packages/core/test/config/agent.test.ts
index 6456e6a20be..8f2f9d83f54 100644
--- a/packages/core/test/config/agent.test.ts
+++ b/packages/core/test/config/agent.test.ts
@@ -119,6 +119,15 @@ permissions:
     }
   }
 
+  it.live("keeps Markdown legacy permission precedence in source order", () =>
+    Effect.gen(function* () {
+      const agent = yield* loadMarkdownAgent('permission:\n  "*": allow\n  bash: ask\n  edit: deny')
+      expect(Permission.evaluate("shell", "ls", agent.permissions).effect).toBe("ask")
+      expect(Permission.evaluate("edit", "example.txt", agent.permissions).effect).toBe("deny")
+      expect(Permission.evaluate("webfetch", "*", agent.permissions).effect).toBe("allow")
+    }),
+  )
+
   for (const variant of [undefined, "high"]) {
     it.live(`loads Markdown legacy temperature ${variant ? "with" : "without"} a separate variant`, () =>
       Effect.gen(function* () {
diff --git a/packages/core/test/config/normalization.test.ts b/packages/core/test/config/normalization.test.ts
index c7ff66bbef1..e5665fad5a2 100644
--- a/packages/core/test/config/normalization.test.ts
+++ b/packages/core/test/config/normalization.test.ts
@@ -240,6 +240,30 @@ describe("ConfigNormalize", () => {
     ])
   })
 
+  test.each(["agent", "mode"])("preserves legacy %s permission source order", (key) => {
+    const permission = { "*": "allow", bash: "ask", custom: "deny", edit: "deny" }
+    expect(normalized({ [key]: { build: { permission } } }).encoded.agents).toMatchObject({
+      build: {
+        permissions: [
+          { action: "*", resource: "*", effect: "allow" },
+          { action: "shell", resource: "*", effect: "ask" },
+          { action: "custom", resource: "*", effect: "deny" },
+          { action: "edit", resource: "*", effect: "deny" },
+        ],
+      },
+    })
+    expect(
+      normalized({ [key]: { review: { permission: { "*": "deny", read: "allow" } } } }).encoded.agents,
+    ).toMatchObject({
+      review: {
+        permissions: [
+          { action: "*", resource: "*", effect: "deny" },
+          { action: "read", resource: "*", effect: "allow" },
+        ],
+      },
+    })
+  })
+
   test("redacts permission resource keys from invalid diagnostics", () => {
     const result = normalized({
       permission: { bash: { "curl -H Authorization:Bearer TOPSECRET *": "bogus" } },