diff --git a/src/usethis/_integrations/project/packages.py b/src/usethis/_integrations/project/packages.py
index 2d0563b7..47c58915 100644
--- a/src/usethis/_integrations/project/packages.py
+++ b/src/usethis/_integrations/project/packages.py
@@ -49,8 +49,8 @@ def _get_packages_in_dir(path: Path) -> set[str]:
     """Get the names of packages in the given directory."""
     return {
         Path(module_name).name
-        for _, module_name, _ in pkgutil.iter_modules([path.as_posix()])
-        if not _is_excluded(module_name)
+        for _, module_name, ispkg in pkgutil.iter_modules([path.as_posix()])
+        if ispkg and not _is_excluded(module_name)
     }
 
 
diff --git a/tests/usethis/_integrations/project/test_packages.py b/tests/usethis/_integrations/project/test_packages.py
index f52d025b..5bef92c2 100644
--- a/tests/usethis/_integrations/project/test_packages.py
+++ b/tests/usethis/_integrations/project/test_packages.py
@@ -62,3 +62,39 @@ def test_multiple_namespace_packages(self, tmp_path: Path):
 
         with change_cwd(tmp_path):
             assert get_importable_packages() == {"foo", "bar"}
+
+    def test_flat_layout_excludes_root_py_files(self, tmp_path: Path):
+        """Test that root-level .py files are excluded in a flat layout.
+
+        In a flat layout (no src/ directory), standalone .py files like
+        setup.py or conftest.py should not be detected as importable packages.
+        Only directories with __init__.py should be included.
+        """
+        (tmp_path / "foo").mkdir()
+        (tmp_path / "foo" / "__init__.py").touch()
+        (tmp_path / "foo" / "bar.py").touch()
+        # Root-level .py files that should be excluded
+        (tmp_path / "setup.py").touch()
+        (tmp_path / "conftest.py").touch()
+
+        with change_cwd(tmp_path):
+            # Should only include "foo" package, not "setup" or "conftest" modules
+            assert get_importable_packages() == {"foo"}
+
+    def test_src_layout_excludes_root_py_files(self, tmp_path: Path):
+        """Test that root-level .py files are excluded in a src/ layout.
+
+        In a src/ layout, standalone .py files in src/ like __init__.py
+        (without a package directory) should not be detected as importable packages.
+        """
+        (tmp_path / "src").mkdir()
+        (tmp_path / "src" / "foo").mkdir()
+        (tmp_path / "src" / "foo" / "__init__.py").touch()
+        (tmp_path / "src" / "foo" / "bar.py").touch()
+        # Root-level .py files in src/ that should be excluded
+        (tmp_path / "src" / "conftest.py").touch()
+        (tmp_path / "src" / "helper.py").touch()
+
+        with change_cwd(tmp_path):
+            # Should only include "foo" package, not "conftest" or "helper" modules
+            assert get_importable_packages() == {"foo"}