@@ -184,16 +184,23 @@ function decode(file: { directory: string; filepath: string; primary: boolean },
     .replace(/\.md$/, "")
   const body = markdown.content.trim()
   const legacy = Object.keys(markdown.data).some((key) => !agentKeys.has(key))
+  // Join legacy model + variant without sending native request/permissions through migration.
+  // Embedded and structured native selections, and a variant without a model, stay unchanged.
+  const data =
+    typeof markdown.data.model === "string" &&
+    !markdown.data.model.includes("#") &&
+    typeof markdown.data.variant === "string" &&
+    /^[^#]+$/.test(markdown.data.variant)
+      ? { ...markdown.data, model: `${markdown.data.model}#${markdown.data.variant}` }
+      : markdown.data
   const agent = legacy
     ? Option.getOrUndefined(
         Option.map(
           decodeLegacyAgent({ name, ...markdown.data, prompt: body }, { errors: "all", propertyOrder: "original" }),
           ConfigMigrateV1.migrateAgent,
         ),
       )
-    : Option.getOrUndefined(
-        decodeAgent({ ...markdown.data, system: body }, { errors: "all", propertyOrder: "original" }),
-      )
+    : Option.getOrUndefined(decodeAgent({ ...data, system: body }, { errors: "all", propertyOrder: "original" }))
   if (!agent) return
   const info = Option.getOrUndefined(
     decodeConfig({
 
@@ -6,6 +6,7 @@ import { Agent } from "@opencode/core/agent"
 import { Bus } from "@opencode/core/bus"
 import { Config } from "@opencode/core/config"
 import { Directory, Document, Event, Info } from "@opencode/schema/config"
+import { Model } from "@opencode/schema/model"
 import { ConfigAgentPlugin } from "@opencode/core/config/plugin/agent"
 import { AppNodeBuilder } from "@opencode/core/effect/app-node-builder"
 import { LayerNode } from "@opencode/util/effect/layer-node"
@@ -17,7 +18,7 @@ import { AbsolutePath } from "@opencode/core/schema"
 import { ConfigMigrateV1 } from "@opencode/core/v1/config/migrate"
 import { ConfigAgentV1 } from "@opencode/core/v1/config/agent"
 import { advance, drain } from "../lib/clock"
-import { tmpdir } from "../fixture/tmpdir"
+import { tmpdir, tmpdirScoped } from "../fixture/tmpdir"
 import { testEffect } from "../lib/effect"
 import { agentHost, host } from "../plugin/host"
 
@@ -60,6 +61,76 @@ test("keeps schema fields and name out of legacy agent options", () => {
 })
 
 describe("ConfigAgentPlugin.Plugin", () => {
+  for (const item of [
+    { name: "separate legacy variant", frontmatter: "model: example/chat\nvariant: high", model: "example/chat#high" },
+    { name: "unqualified model", frontmatter: "model: example/chat", model: "example/chat" },
+    { name: "embedded native variant", frontmatter: "model: example/chat#high", model: "example/chat#high" },
+    {
+      name: "structured native variant",
+      frontmatter: "model:\n  providerID: example\n  model: chat\n  variant: high",
+      model: "example/chat#high",
+    },
+    {
+      name: "structured unqualified model",
+      frontmatter: "model:\n  providerID: example\n  model: chat",
+      model: "example/chat",
+    },
+    { name: "standalone variant", frontmatter: "variant: high", model: undefined },
+    {
+      name: "embedded native variant with an ignored separate variant",
+      frontmatter: "model: example/chat#high\nvariant: low",
+      model: "example/chat#high",
+    },
+    {
+      name: "structured native variant with an ignored separate variant",
+      frontmatter: "model:\n  providerID: example\n  model: chat\n  variant: high\nvariant: low",
+      model: "example/chat#high",
+    },
+  ]) {
+    for (const native of [false, true]) {
+      it.live(`loads Markdown ${item.name}${native ? " with native request and permissions" : ""}`, () =>
+        Effect.gen(function* () {
+          const agent = yield* loadMarkdownAgent(
+            native
+              ? `${item.frontmatter}
+request:
+  headers:
+    x-agent: native
+  body:
+    effort: high
+permissions:
+  - action: edit
+    resource: "*"
+    effect: deny`
+              : item.frontmatter,
+          )
+          expect(agent.model).toEqual(item.model === undefined ? undefined : Model.Ref.parse(item.model))
+          expect(agent.request).toEqual({
+            settings: {},
+            headers: native ? { "x-agent": "native" } : {},
+            body: native ? { effort: "high" } : {},
+          })
+          if (native) {
+            expect(agent.permissions).toContainEqual({ action: "edit", resource: "*", effect: "deny" })
+            expect(Permission.evaluate("edit", "example.txt", agent.permissions).effect).toBe("deny")
+          }
+        }),
+      )
+    }
+  }
+
+  for (const variant of [undefined, "high"]) {
+    it.live(`loads Markdown legacy temperature ${variant ? "with" : "without"} a separate variant`, () =>
+      Effect.gen(function* () {
+        const agent = yield* loadMarkdownAgent(
+          `model: example/chat\ntemperature: 0.5${variant ? `\nvariant: ${variant}` : ""}`,
+        )
+        expect(agent.model).toEqual(Model.Ref.parse(variant ? "example/chat#high" : "example/chat"))
+        expect(agent.request).toEqual({ settings: {}, headers: {}, body: { temperature: 0.5 } })
+      }),
+    )
+  }
+
   it.effect("matches POSIX paths against home-relative permissions", () =>
     Effect.gen(function* () {
       const permissions = yield* loadHomePermissions("/home/test")
@@ -560,6 +631,26 @@ Use native v2 fields.`,
   )
 })
 
+function loadMarkdownAgent(frontmatter: string) {
+  return Effect.gen(function* () {
+    const tmp = yield* tmpdirScoped()
+    const fs = yield* FSUtil.Service
+    yield* fs.makeDirectory(path.join(tmp.path, "agents"))
+    yield* fs.writeFileString(
+      path.join(tmp.path, "agents", "reviewer.md"),
+      `---\n${frontmatter}\n---\nReview carefully.`,
+    )
+    const agents = yield* Agent.Service
+    yield* ConfigAgentPlugin.Plugin.effect(host({ agent: agentHost(agents) })).pipe(
+      Effect.provide(Config.testLayer([directoryEntry(tmp.path)])),
+    )
+    const agent = yield* agents.get(Agent.ID.make("reviewer"))
+    if (!agent) throw new Error("expected configured Markdown agent")
+    expect(agent.system).toBe("Review carefully.")
+    return agent
+  })
+}
+
 function directoryEntry(directory: string) {
   return new Directory({ type: "directory", path: AbsolutePath.make(directory) })
 }