diff --git a/changelog/14454.bugfix.rst b/changelog/14454.bugfix.rst
new file mode 100644
index 00000000000..005a1c29259
--- /dev/null
+++ b/changelog/14454.bugfix.rst
@@ -0,0 +1 @@
+Fixed a regression where :option:`-c` pointing to a config file in a sub-directory would set :confval:`rootdir` to the config file's parent directory instead of the invocation directory, breaking conftest discovery. Patch by :user:`EternalRights`.
diff --git a/src/_pytest/config/__init__.py b/src/_pytest/config/__init__.py
index 44d606b00a4..f7f04117be1 100644
--- a/src/_pytest/config/__init__.py
+++ b/src/_pytest/config/__init__.py
@@ -22,6 +22,7 @@
 import importlib
 import importlib.metadata
 import inspect
+import logging
 import os
 import pathlib
 import re
@@ -78,6 +79,9 @@
 from _pytest.warning_types import warn_explicit_for
 
 
+log = logging.getLogger(__name__)
+
+
 if TYPE_CHECKING:
     from _pytest.assertion.rewrite import AssertionRewritingHook
     from _pytest.cacheprovider import Cache
@@ -1501,6 +1505,14 @@ def parse(self, args: list[str], addopts: bool = True) -> None:
         self._parser.extra_info["rootdir"] = str(self.rootpath)
         self._parser.extra_info["inifile"] = str(self.inipath)
 
+        if ns.inifilename and not ns.rootdir:
+            if inipath is not None and inipath.parent != self.invocation_params.dir:
+                log.warning(
+                    "rootdir was set to %s because -c was given without --rootdir. "
+                    "Use --rootdir to explicitly disambiguate.",
+                    self.invocation_params.dir,
+                )
+
         self._parser.addini("addopts", "Extra command line options", "args")
         self._parser.addini("minversion", "Minimally required pytest version")
         self._parser.addini(
diff --git a/src/_pytest/config/findpaths.py b/src/_pytest/config/findpaths.py
index e74546c6e28..3950a895299 100644
--- a/src/_pytest/config/findpaths.py
+++ b/src/_pytest/config/findpaths.py
@@ -308,7 +308,7 @@ def determine_setup(
         inipath: Path | None = inipath_
         inicfg = load_config_dict_from_file(inipath_) or {}
         if rootdir_cmd_arg is None:
-            rootdir = inipath_.parent
+            rootdir = invocation_dir
     else:
         ancestor = get_common_ancestor(invocation_dir, dirs)
         rootdir, inipath, inicfg, ignored_config_files = locate_config(
diff --git a/testing/test_config.py b/testing/test_config.py
index 8026c108db0..ec976786430 100644
--- a/testing/test_config.py
+++ b/testing/test_config.py
@@ -2028,12 +2028,73 @@ def test_with_specific_inifile(
             override_ini=None,
             args=[str(tmp_path)],
             rootdir_cmd_arg=None,
-            invocation_dir=Path.cwd(),
+            invocation_dir=tmp_path,
         )
         assert rootpath == tmp_path
         assert inipath == p
         assert ini_config["x"] == ConfigValue("10", origin="file", mode="ini")
 
+    def test_config_in_subdir_does_not_change_rootdir(
+        self, tmp_path: Path, monkeypatch: pytest.MonkeyPatch
+    ) -> None:
+        """Config file in a subdir should not move rootdir to that subdir (#13246)."""
+        config_dir = tmp_path / "config"
+        config_dir.mkdir()
+        inipath = config_dir / "pytest.ini"
+        inipath.touch()
+        monkeypatch.chdir(tmp_path)
+
+        rootpath, found_inipath, *_ = determine_setup(
+            inifile=str(inipath),
+            override_ini=None,
+            args=[],
+            rootdir_cmd_arg=None,
+            invocation_dir=Path.cwd(),
+        )
+        assert rootpath == tmp_path, (
+            f"rootdir should be invocation_dir ({tmp_path}), got {rootpath}"
+        )
+        assert found_inipath == inipath
+
+    def test_rootdir_warning_when_config_in_subdir(
+        self, tmp_path: Path, caplog: pytest.LogCaptureFixture
+    ) -> None:
+        """When -c points to a subdir, a warning should be logged (#13246)."""
+        import logging
+
+        config_dir = tmp_path / "config"
+        config_dir.mkdir()
+        inipath = config_dir / "pytest.ini"
+        inipath.touch()
+
+        caplog.set_level(logging.WARNING)
+        Config.fromdictargs(
+            {"inifilename": str(inipath)},  # -c config/pytest.ini
+            [],
+        )
+
+        assert len(caplog.records) >= 1
+        assert "rootdir was set to" in caplog.records[0].message
+        assert "--rootdir" in caplog.records[0].message
+
+    def test_no_warning_when_config_in_rootdir(
+        self, tmp_path: Path, monkeypatch: MonkeyPatch, caplog: pytest.LogCaptureFixture
+    ) -> None:
+        """When -c points to the invocation dir itself, no warning needed (#13246)."""
+        import logging
+
+        inipath = tmp_path / "pytest.ini"
+        inipath.touch()
+        monkeypatch.chdir(tmp_path)
+
+        caplog.set_level(logging.WARNING)
+        Config.fromdictargs(
+            {"inifilename": str(inipath)},
+            [],
+        )
+
+        assert len(caplog.records) == 0
+
     def test_explicit_config_file_sets_rootdir(
         self, tmp_path: Path, monkeypatch: pytest.MonkeyPatch
     ) -> None: