diff --git a/apps/server/src/orchestration-v2/Adapters/CodexAdapterV2.test.ts b/apps/server/src/orchestration-v2/Adapters/CodexAdapterV2.test.ts
index 21b398cdc7ad..7b12dc2ae036 100644
--- a/apps/server/src/orchestration-v2/Adapters/CodexAdapterV2.test.ts
+++ b/apps/server/src/orchestration-v2/Adapters/CodexAdapterV2.test.ts
@@ -640,12 +640,10 @@ describe("CodexAdapterV2 process spawning", () => {
           model: "gpt-5.4",
           config: {
             "tools.update_plan.enabled": true,
-            mcp_servers: {
-              "t3-code": {
-                url: "http://127.0.0.1:43123/mcp",
-                http_headers: {
-                  Authorization: "Bearer secret-codex-token",
-                },
+            "mcp_servers.t3-code": {
+              url: "http://127.0.0.1:43123/mcp",
+              http_headers: {
+                Authorization: "Bearer secret-codex-token",
               },
             },
           },
diff --git a/apps/server/src/orchestration-v2/Adapters/CodexAdapterV2.ts b/apps/server/src/orchestration-v2/Adapters/CodexAdapterV2.ts
index 2256f4ff9e99..2bfa47694530 100644
--- a/apps/server/src/orchestration-v2/Adapters/CodexAdapterV2.ts
+++ b/apps/server/src/orchestration-v2/Adapters/CodexAdapterV2.ts
@@ -1216,12 +1216,12 @@ export function codexThreadRuntimeParams(input: {
       ...(mcpSession === undefined
         ? {}
         : {
-            mcp_servers: {
-              "t3-code": {
-                url: mcpSession.endpoint,
-                http_headers: {
-                  Authorization: mcpSession.authorizationHeader,
-                },
+            // Dotted key: thread config shares Codex's `-c` override layer, so a
+            // whole `mcp_servers` table would replace servers added by launch args.
+            "mcp_servers.t3-code": {
+              url: mcpSession.endpoint,
+              http_headers: {
+                Authorization: mcpSession.authorizationHeader,
               },
             },
           }),
diff --git a/packages/effect-codex-app-server/src/replay.ts b/packages/effect-codex-app-server/src/replay.ts
index 1c98c7bc3b8a..d8b3f3aee950 100644
--- a/packages/effect-codex-app-server/src/replay.ts
+++ b/packages/effect-codex-app-server/src/replay.ts
@@ -273,7 +273,11 @@ function normalizeThreadRequest(frame: unknown, ignoredConfigKeys: ReadonlySet<s
   }
   const { cwd: _cwd, model: _model, config, ...params } = record.params as Record<string, unknown>;
   if (typeof config !== "object" || config === null) return { ...record, params };
-  const { mcp_servers: _mcpServers, ...owned } = config as Record<string, unknown>;
+  const owned = Object.fromEntries(
+    Object.entries(config as Record<string, unknown>).filter(
+      ([key]) => key !== "mcp_servers" && !key.startsWith("mcp_servers."),
+    ),
+  );
   for (const key of ignoredConfigKeys) delete owned[key];
   return { ...record, params: { ...params, config: owned } };
 }