diff --git a/server/src/chat/transport/matrix/bot/context.rs b/server/src/chat/transport/matrix/bot/context.rs
index b964a864..1cb67a97 100644
--- a/server/src/chat/transport/matrix/bot/context.rs
+++ b/server/src/chat/transport/matrix/bot/context.rs
@@ -114,7 +114,10 @@ impl BotContext {
         match client.post(&url).json(&body).send().await {
             Ok(resp) if resp.status().is_success() => {
                 match resp.json::<serde_json::Value>().await {
-                    Ok(json) => json.get("response").and_then(|v| v.as_str()).map(String::from),
+                    Ok(json) => json
+                        .get("response")
+                        .and_then(|v| v.as_str())
+                        .map(String::from),
                     Err(e) => Some(format!("Failed to parse response from project server: {e}")),
                 }
             }
diff --git a/server/src/chat/transport/matrix/bot/messages.rs b/server/src/chat/transport/matrix/bot/messages.rs
index f0cde960..481a891a 100644
--- a/server/src/chat/transport/matrix/bot/messages.rs
+++ b/server/src/chat/transport/matrix/bot/messages.rs
@@ -207,8 +207,10 @@ pub(super) async fn on_room_message(
             && (crate::chat::commands::commands()
                 .iter()
                 .any(|c| c.name == cmd)
-                || ["assign", "start", "delete", "rebuild", "rmtree", "htop", "timer"]
-                    .contains(&cmd.as_str()));
+                || [
+                    "assign", "start", "delete", "rebuild", "rmtree", "htop", "timer",
+                ]
+                .contains(&cmd.as_str()));
 
         if is_known_command {
             // Proxy to the active project server.
@@ -643,12 +645,18 @@ pub(super) async fn handle_message(
     let sent_any_chunk = Arc::new(AtomicBool::new(false));
     let sent_any_chunk_for_callback = Arc::clone(&sent_any_chunk);
 
-    // In gateway mode, run Claude Code in the active project's directory.
-    let project_root_str = ctx
-        .effective_project_root()
-        .await
-        .to_string_lossy()
-        .to_string();
+    // In gateway mode, run Claude Code in the gateway config directory so it
+    // picks up the `.mcp.json` that points to the gateway's MCP proxy endpoint.
+    // The gateway proxies tool calls to the active project automatically.
+    // In standalone mode, use the project root directly.
+    let project_root_str = if ctx.is_gateway() {
+        ctx.project_root.to_string_lossy().to_string()
+    } else {
+        ctx.effective_project_root()
+            .await
+            .to_string_lossy()
+            .to_string()
+    };
     let chat_fut = provider.chat_stream(
         &prompt,
         &project_root_str,