diff --git a/src/CodexAcpClient.ts b/src/CodexAcpClient.ts
index 8a5af9e7..f7474e9d 100644
--- a/src/CodexAcpClient.ts
+++ b/src/CodexAcpClient.ts
@@ -758,9 +758,15 @@ export class CodexAcpClient {
         }));
         let serversToConfigure = requestedServers;
         if (shouldDeduplicateMcpConflicts()) {
-            // Prevents Codex from deep-merging incompatible field types, such as url and stdio schemas.
-            const existingNames = await this.getConfigMcpServerNames(projectPath);
-            serversToConfigure = requestedServers.filter(mcp => !existingNames.has(mcp.name));
+            // Codex deep-merges session config into its persisted config. Let the session replace
+            // connection details when both definitions use the same transport, but keep filtering
+            // incompatible transports because merging e.g. `url` and `command` produces an invalid
+            // hybrid definition.
+            const existingServers = await this.getConfigMcpServers(projectPath);
+            serversToConfigure = requestedServers.filter(mcp => {
+                const existing = existingServers.get(mcp.name);
+                return existing === undefined || haveCompatibleMcpTransports(existing, mcp.server);
+            });
         }
         if (serversToConfigure.length === 0) {
             return configWithWorkspaceRoots;
@@ -772,7 +778,7 @@ export class CodexAcpClient {
         };
     }
 
-    private async getConfigMcpServerNames(projectPath: string): Promise<Set<string>> {
+    private async getConfigMcpServers(projectPath: string): Promise<Map<string, JsonObject>> {
         const response = await this.codexClient.configRead({ includeLayers: true, cwd: projectPath });
         const effectiveMcpServers = response?.config?.["mcp_servers"];
         const configLayers = response?.layers ?? [];
@@ -780,10 +786,15 @@ export class CodexAcpClient {
             return isJsonObject(layer.config) ? layer.config["mcp_servers"] : undefined;
         });
         const configuredMcpServers = [effectiveMcpServers, ...layerMcpServers].filter(isJsonObject);
-        if (configuredMcpServers.length === 0) {
-            return new Set();
+        const servers = new Map<string, JsonObject>();
+        for (const configured of configuredMcpServers) {
+            for (const [name, server] of Object.entries(configured)) {
+                if (!servers.has(name) && isJsonObject(server)) {
+                    servers.set(name, server);
+                }
+            }
         }
-        return new Set(configuredMcpServers.flatMap(server => Object.keys(server)));
+        return servers;
     }
 
     getModelProvider(): string | null {
@@ -1218,6 +1229,16 @@ function shouldDeduplicateMcpConflicts(): boolean {
     return !disabledByEnv;
 }
 
+function haveCompatibleMcpTransports(configured: JsonObject, requested: McpServer): boolean {
+    const configuredTransport = "command" in configured && !("url" in configured)
+        ? "stdio"
+        : "url" in configured && !("command" in configured)
+            ? "http"
+            : null;
+    const requestedTransport = "type" in requested ? requested.type : "stdio";
+    return configuredTransport === requestedTransport;
+}
+
 type WireApi = "responses";
 
 type GatewayConfigSource = "authentication" | "acpProviders";
diff --git a/src/__tests__/CodexACPAgent/CodexAcpClient.test.ts b/src/__tests__/CodexACPAgent/CodexAcpClient.test.ts
index 77aa7af7..be118fe7 100644
--- a/src/__tests__/CodexACPAgent/CodexAcpClient.test.ts
+++ b/src/__tests__/CodexACPAgent/CodexAcpClient.test.ts
@@ -886,7 +886,7 @@ describe('ACP server test', { timeout: 40_000 }, () => {
         } as unknown as acp.NewSessionRequest)).rejects.toThrow("additionalDirectories entries must be strings");
     });
 
-    it('sanitizes whitespace in ACP MCP server names before adding them to Codex config', async () => {
+    it('adds same-transport ACP MCP overrides while filtering incompatible conflicts', async () => {
         const mockFixture = createCodexMockTestFixture();
         const codexAcpClient = mockFixture.getCodexAcpClient();
         const codexAppServerClient = mockFixture.getCodexAppServerClient();
@@ -898,6 +898,13 @@ describe('ACP server test', { timeout: 40_000 }, () => {
                     shared_mcp: {
                         url: "https://example.com/mcp",
                     },
+                    stdio_server_one: {
+                        command: "stale-command",
+                        args: ["stale"],
+                    },
+                    global_only: {
+                        command: "global-command",
+                    },
                 },
             },
         } as any);
diff --git a/src/__tests__/CodexACPAgent/mcp-config-merge.test.ts b/src/__tests__/CodexACPAgent/mcp-config-merge.test.ts
index 94a92d71..190c3c1f 100644
--- a/src/__tests__/CodexACPAgent/mcp-config-merge.test.ts
+++ b/src/__tests__/CodexACPAgent/mcp-config-merge.test.ts
@@ -17,9 +17,18 @@ describe('MCP config merge across configured MCP servers and ACP request', { tim
     beforeEach(() => {
         vi.clearAllMocks();
 
+        const node = JSON.stringify(process.execPath);
+        const mcpServer = JSON.stringify(path.resolve(process.cwd(), "node_modules/mcp-hello-world/build/stdio.js"));
         const globalConfig = `
 [mcp_servers.shared-mcp]
 url = "https://example.com/mcp"
+
+[mcp_servers.same-transport]
+command = "missing-global-command"
+
+[mcp_servers.global-only]
+command = ${node}
+args = [${mcpServer}]
 `;
 
         const projectConfig = `
@@ -97,6 +106,37 @@ url = "https://example.com/mcp"
         })).resolves.toBeDefined();
     });
 
+    it('should prefer a same-transport ACP MCP and preserve unrelated configured servers', async () => {
+        const codexAcpAgent = fixture.getCodexAcpAgent();
+        await codexAcpAgent.initialize({protocolVersion: 1});
+        fixture.getCodexAcpClient().authRequired = vi.fn().mockResolvedValue(false);
+
+        const codexAcpClient = fixture.getCodexAcpClient();
+        const startupVersion = codexAcpClient.getMcpServerStartupVersion();
+        const mcpServer = path.resolve(process.cwd(), "node_modules/mcp-hello-world/build/stdio.js");
+        await codexAcpAgent.newSession({
+            cwd: "",
+            mcpServers: [{
+                name: "same-transport",
+                command: process.execPath,
+                args: [mcpServer],
+                env: [],
+            }],
+        });
+
+        await expect(codexAcpClient.awaitMcpServerStartup(["same-transport"], startupVersion)).resolves.toEqual({
+            ready: ["same-transport"],
+            failed: [],
+            cancelled: [],
+        });
+        await expect(codexAcpClient.listMcpServers()).resolves.toMatchObject({
+            data: expect.arrayContaining([
+                expect.objectContaining({name: "same-transport"}),
+                expect.objectContaining({name: "global-only"}),
+            ]),
+        });
+    });
+
     it('should not filter the conflicting ACP MCP when config filtering is disabled', async () => {
         vi.stubEnv("DISABLE_MCP_CONFIG_FILTERING", "true");
         const codexAcpAgent = fixture.getCodexAcpAgent();