diff --git a/src/infra_controller/discovery.py b/src/infra_controller/discovery.py
index 9958c2d..7575d16 100644
--- a/src/infra_controller/discovery.py
+++ b/src/infra_controller/discovery.py
@@ -139,6 +139,8 @@ class DiscoveryManager:
 
         for link_file in list(watch_path.glob("*.yml")) + list(watch_path.glob("*.yaml")):
             try:
+                if (watch_path / f"{link_file.stem}.toml").exists():
+                    continue
                 if link_file.stem in apps:
                     continue
 
@@ -166,6 +168,8 @@ class DiscoveryManager:
             if not base_path.exists():
                 continue
 
+            toml_dirs: set[Path] = set()
+
             for infra_file in base_path.rglob(".infra.toml"):
                 if self._should_exclude(infra_file):
                     continue
@@ -180,13 +184,19 @@ class DiscoveryManager:
                         last_seen=datetime.now(),
                         discovery_method="scan",
                     )
+                    toml_dirs.add(infra_file.parent)
                     logger.info("Discovered app via scan: %s", md.project)
                 except Exception as e:
                     logger.error("Error reading %s: %s", infra_file, e)
 
-            for infra_file in base_path.rglob(".infra.yml"):
+            for infra_file in list(base_path.rglob(".infra.yml")) + list(base_path.rglob(".infra.yaml")):
                 if self._should_exclude(infra_file):
                     continue
+                if infra_file.parent in toml_dirs:
+                    continue
+                if not self._is_active_project(infra_file.parent):
+                    continue
+
                 try:
                     md = InfraMetadata.from_file(infra_file)
                 except Exception as e:
@@ -195,8 +205,6 @@ class DiscoveryManager:
 
                 if md.project in apps:
                     continue
-                if not self._is_active_project(infra_file.parent):
-                    continue
 
                 apps[md.project] = AppRegistration(
                     name=md.project,
diff --git a/tests/test_infra_metadata.py b/tests/test_infra_metadata.py
index 03103c9..9f9caf7 100644
--- a/tests/test_infra_metadata.py
+++ b/tests/test_infra_metadata.py
@@ -4,7 +4,9 @@ from pathlib import Path
 
 import pytest
 
+from infra_controller.config import DiscoveryConfig
 from infra_controller.discovery import InfraMetadata
+from infra_controller.discovery import DiscoveryManager
 
 
 def _write(path: Path, content: str) -> Path:
@@ -112,3 +114,35 @@ requires:
 
     with pytest.raises(ValueError, match=r"requires\.services"):
         InfraMetadata.from_file(p)
+
+
+def test_discover_scan_prefers_toml_over_yaml_in_same_dir(tmp_path: Path, monkeypatch) -> None:
+    base = tmp_path / "apps"
+    proj = base / "proj"
+    (proj / ".git").mkdir(parents=True)
+    (proj / ".git" / "HEAD").write_text("ref: refs/heads/main\n", encoding="utf-8")
+
+    _write(
+        proj / ".infra.toml",
+        """
+project = "proj"
+
+[requires]
+services = ["svc_toml"]
+""".lstrip(),
+    )
+    _write(
+        proj / ".infra.yml",
+        """
+project: proj
+requires:
+  services: svc_yaml
+""".lstrip(),
+    )
+
+    cfg = DiscoveryConfig(scan_enabled=True, scan_paths=[base], file_based_enabled=False)
+    mgr = DiscoveryManager(cfg)
+
+    apps = mgr.discover_all()
+    assert set(apps.keys()) == {"proj"}
+    assert apps["proj"].metadata.requires["services"] == ["svc_toml"]