diff --git a/server/src/config.rs b/server/src/config.rs
index 382f2e4..b5f933b 100644
--- a/server/src/config.rs
+++ b/server/src/config.rs
@@ -226,6 +226,11 @@ impl ProjectConfig {
             args.push(render(sp));
         }
 
+        // Explicitly set the project directory so Claude Code doesn't
+        // resolve the main checkout via .git worktree indirection.
+        args.push("--directory".to_string());
+        args.push(worktree_path.to_string());
+
         Ok((command, args, prompt))
     }
 }
@@ -390,7 +395,8 @@ max_turns = 0
             .render_agent_args("/tmp/wt", "42_foo", None, None)
             .unwrap();
         assert_eq!(cmd, "claude");
-        assert!(args.is_empty());
+        assert!(args.contains(&"--directory".to_string()));
+        assert!(args.contains(&"/tmp/wt".to_string()));
         assert!(prompt.contains("42_foo"));
     }