diff --git a/changelog.d/+empty-native-section.bugfix.md b/changelog.d/+empty-native-section.bugfix.md
new file mode 100644
index 0000000..fd6ddff
--- /dev/null
+++ b/changelog.d/+empty-native-section.bugfix.md
@@ -0,0 +1 @@
+Honor an empty native TOML environment section over INI `env` settings.
diff --git a/src/pytest_env/plugin.py b/src/pytest_env/plugin.py
index 61f8c81..d32f5e8 100644
--- a/src/pytest_env/plugin.py
+++ b/src/pytest_env/plugin.py
@@ -232,9 +232,8 @@ def _load_values(early_config: pytest.Config) -> Iterator[Entry]:
     """Load env entries from config, preferring TOML over INI."""
     if toml_config := _find_toml_config(early_config):
         _, entries, _ = _load_toml_config(toml_config)
-        if entries:
-            yield from entries
-            return
+        yield from entries
+        return
 
     for line in early_config.getini("env"):
         # INI lines e.g. D:R:NAME=VAL has two flags (R and D), NAME key, and VAL value
diff --git a/tests/test_env.py b/tests/test_env.py
index 8d38098..6de592c 100644
--- a/tests/test_env.py
+++ b/tests/test_env.py
@@ -226,6 +226,33 @@ def test_env_via_pytest(
             ".pytest.toml",
             id="hidden pytest toml native over ini",
         ),
+        pytest.param(
+            {},
+            "[tool.pytest_env]\n",
+            "",
+            "[pytest]\nenv = FROM_INI=unexpected",
+            {"FROM_INI": None},
+            None,
+            id="empty pyproject native over ini",
+        ),
+        pytest.param(
+            {},
+            "",
+            "[pytest_env]\n",
+            "[pytest]\nenv = FROM_INI=unexpected",
+            {"FROM_INI": None},
+            "pytest.toml",
+            id="empty pytest toml native over ini",
+        ),
+        pytest.param(
+            {},
+            "",
+            "[pytest_env]\n",
+            "[pytest]\nenv = FROM_INI=unexpected",
+            {"FROM_INI": None},
+            ".pytest.toml",
+            id="empty hidden pytest toml native over ini",
+        ),
         pytest.param(
             {},
             '[tool.pytest_env]\nMAGIC = {value = "toml", "transform"= true, "skip_if_set" = true}',
@@ -316,9 +343,8 @@ def test_env_via_toml(
         "PYTEST_DISABLE_PLUGIN_AUTOLOAD": "1",
         "PYTEST_PLUGINS": "pytest_env.plugin",
     }
-
     with mock.patch.dict(os.environ, new_env, clear=True):
-        result = pytester.runpytest(str(test_dir))
+        result = pytester.runpytest(*(("-c", str(pytester.path / "pytest.ini")) if ini else ()), str(test_dir))
 
     result.assert_outcomes(passed=1)