diff --git a/doc/api/esmvalcore.config.rst b/doc/api/esmvalcore.config.rst
index 9b01587263..231140effd 100644
--- a/doc/api/esmvalcore.config.rst
+++ b/doc/api/esmvalcore.config.rst
@@ -88,6 +88,13 @@ To load the configuration object from custom directories, use:
     >>> dirs = ['my/default/config', 'my/custom/config']
     >>> CFG.load_from_dirs(dirs)
 
+To update the existing configuration object from custom directories, use:
+
+.. code-block:: python
+
+    >>> dirs = ['my/default/config', 'my/custom/config']
+    >>> CFG.update_from_dirs(dirs)
+
 
 Session
 *******
diff --git a/esmvalcore/_main.py b/esmvalcore/_main.py
index d0bd6fcf10..451f228ae8 100755
--- a/esmvalcore/_main.py
+++ b/esmvalcore/_main.py
@@ -403,7 +403,6 @@ def run(self, recipe, **kwargs):
 
         """
         from .config import CFG
-        from .config._config_object import _get_all_config_dirs
         from .exceptions import InvalidConfigParameter
 
         cli_config_dir = kwargs.pop("config_dir", None)
@@ -427,10 +426,9 @@ def run(self, recipe, **kwargs):
 
         # New in v2.12.0: read additional configuration directory given by CLI
         # argument
-        if CFG.get("config_file") is None:  # remove in v2.14.0
-            config_dirs = _get_all_config_dirs(cli_config_dir)
+        if CFG.get("config_file") is None and cli_config_dir is not None:
             try:
-                CFG.load_from_dirs(config_dirs)
+                CFG.update_from_dirs([cli_config_dir])
 
             # Potential errors must come from --config_dir (i.e.,
             # cli_config_dir) since other sources have already been read (and
@@ -458,8 +456,8 @@ def run(self, recipe, **kwargs):
 
         # New in v2.12.0
         else:
-            config_dirs = _get_all_config_dirs(cli_config_dir)  # remove v2.14
-            CFG.load_from_dirs(config_dirs)
+            if cli_config_dir is not None:
+                CFG.update_from_dirs([cli_config_dir])
 
     @staticmethod
     def _create_session_dir(session):
diff --git a/esmvalcore/config/_config_object.py b/esmvalcore/config/_config_object.py
index dfe784ef58..baa344f829 100644
--- a/esmvalcore/config/_config_object.py
+++ b/esmvalcore/config/_config_object.py
@@ -317,8 +317,17 @@ def load_from_file(
         self.clear()
         self.update(Config._load_user_config(filename))
 
+    @staticmethod
+    def _get_config_dict_from_dirs(dirs: Iterable[str | Path]) -> dict:
+        """Get configuration :obj:`dict` from directories."""
+        dirs_str: list[str] = []
+        for config_dir in dirs:
+            config_dir = Path(config_dir).expanduser().absolute()
+            dirs_str.append(str(config_dir))
+        return dask.config.collect(paths=dirs_str, env={})
+
     def load_from_dirs(self, dirs: Iterable[str | Path]) -> None:
-        """Load configuration object from directories.
+        """Clear and load configuration object from directories.
 
         This searches for all YAML files within the given directories and
         merges them together using :func:`dask.config.collect`. Nested objects
@@ -344,23 +353,17 @@ def load_from_dirs(self, dirs: Iterable[str | Path]) -> None:
             Invalid configuration option given.
 
         """
-        dirs_str: list[str] = []
-
         # Always consider default options; these have the lowest priority
-        dirs_str.append(str(DEFAULT_CONFIG_DIR))
+        dirs = [DEFAULT_CONFIG_DIR] + list(dirs)
 
-        for config_dir in dirs:
-            config_dir = Path(config_dir).expanduser().absolute()
-            dirs_str.append(str(config_dir))
-
-        new_config_dict = dask.config.collect(paths=dirs_str, env={})
+        new_config_dict = self._get_config_dict_from_dirs(dirs)
         self.clear()
         self.update(new_config_dict)
 
         self.check_missing()
 
     def reload(self) -> None:
-        """Reload the configuration object.
+        """Clear and reload the configuration object.
 
         This will read all YAML files in the user configuration directory (by
         default ``~/.config/esmvaltool``, but this can be changed with the
@@ -431,6 +434,39 @@ def start_session(self, name: str) -> Session:
             session = Session(config=self.copy(), name=name)
         return session
 
+    def update_from_dirs(self, dirs: Iterable[str | Path]) -> None:
+        """Update configuration object from directories.
+
+        This will first search for all YAML files within the given directories
+        and merge them together using :func:`dask.config.collect` (if identical
+        values are provided in multiple files, the value from the last file
+        will be used).  Then, the current configuration is merged with these
+        new configuration options using :func:`dask.config.merge` (new values
+        are preferred over old values). Nested objects are properly considered;
+        see :func:`dask.config.update` for details.
+
+        Note
+        ----
+        Just like :func:`dask.config.collect`, this silently ignores
+        non-existing directories.
+
+        Parameters
+        ----------
+        dirs:
+            A list of directories to search for YAML configuration files.
+
+        Raises
+        ------
+        esmvalcore.exceptions.InvalidConfigParameter
+            Invalid configuration option given.
+
+        """
+        new_config_dict = self._get_config_dict_from_dirs(dirs)
+        merged_config_dict = dask.config.merge(self, new_config_dict)
+        self.update(merged_config_dict)
+
+        self.check_missing()
+
 
 class Session(ValidatedConfig):
     """Container class for session configuration and directory information.
diff --git a/tests/unit/config/test_config_object.py b/tests/unit/config/test_config_object.py
index fa6c3111b3..1c3f36b033 100644
--- a/tests/unit/config/test_config_object.py
+++ b/tests/unit/config/test_config_object.py
@@ -393,33 +393,8 @@ def test_get_global_config_deprecated(mocker, tmp_path):
     assert cfg["output_dir"] == Path("/new/output/dir")
 
 
-@pytest.mark.parametrize(
-    "dirs,output_file_type,rootpath",
-    [
-        ([], "png", {"default": "~/climate_data"}),
-        (["/this/path/does/not/exist"], "png", {"default": "~/climate_data"}),
-        (["{tmp_path}/config1"], "1", {"default": "1", "1": "1"}),
-        (
-            ["{tmp_path}/config1", "/this/path/does/not/exist"],
-            "1",
-            {"default": "1", "1": "1"},
-        ),
-        (
-            ["{tmp_path}/config1", "{tmp_path}/config2"],
-            "2b",
-            {"default": "2b", "1": "1", "2": "2b"},
-        ),
-        (
-            ["{tmp_path}/config2", "{tmp_path}/config1"],
-            "1",
-            {"default": "1", "1": "1", "2": "2b"},
-        ),
-    ],
-)
-def test_load_from_dirs_always_default(
-    dirs, output_file_type, rootpath, tmp_path
-):
-    """Test `Config.load_from_dirs`."""
+def _setup_config_dirs(tmp_path):
+    """Setup test configuration directories."""
     config1 = tmp_path / "config1" / "1.yml"
     config2a = tmp_path / "config2" / "2a.yml"
     config2b = tmp_path / "config2" / "2b.yml"
@@ -456,6 +431,36 @@ def test_load_from_dirs_always_default(
         )
     )
 
+
+@pytest.mark.parametrize(
+    "dirs,output_file_type,rootpath",
+    [
+        ([], "png", {"default": "~/climate_data"}),
+        (["/this/path/does/not/exist"], "png", {"default": "~/climate_data"}),
+        (["{tmp_path}/config1"], "1", {"default": "1", "1": "1"}),
+        (
+            ["{tmp_path}/config1", "/this/path/does/not/exist"],
+            "1",
+            {"default": "1", "1": "1"},
+        ),
+        (
+            ["{tmp_path}/config1", "{tmp_path}/config2"],
+            "2b",
+            {"default": "2b", "1": "1", "2": "2b"},
+        ),
+        (
+            ["{tmp_path}/config2", "{tmp_path}/config1"],
+            "1",
+            {"default": "1", "1": "1", "2": "2b"},
+        ),
+    ],
+)
+def test_load_from_dirs_always_default(
+    dirs, output_file_type, rootpath, tmp_path
+):
+    """Test `Config.load_from_dirs`."""
+    _setup_config_dirs(tmp_path)
+
     config_dirs = []
     for dir_ in dirs:
         config_dirs.append(dir_.format(tmp_path=str(tmp_path)))
@@ -465,11 +470,14 @@ def test_load_from_dirs_always_default(
 
     cfg = Config()
     assert not cfg
+    cfg["rootpath"] = {"X": "x"}
+    cfg["search_esgf"] = "when_missing"
 
     cfg.load_from_dirs(config_dirs)
 
     assert cfg["output_file_type"] == output_file_type
     assert cfg["rootpath"] == rootpath
+    assert cfg["search_esgf"] == "never"
 
 
 @pytest.mark.parametrize(
@@ -514,3 +522,52 @@ def test_get_all_config_sources(cli_config_dir, output, monkeypatch):
         cli_config_dir
     )
     assert config_srcs == output
+
+
+@pytest.mark.parametrize(
+    "dirs,output_file_type,rootpath",
+    [
+        ([], None, {"X": "x"}),
+        (["/this/path/does/not/exist"], None, {"X": "x"}),
+        (["{tmp_path}/config1"], "1", {"default": "1", "1": "1", "X": "x"}),
+        (
+            ["{tmp_path}/config1", "/this/path/does/not/exist"],
+            "1",
+            {"default": "1", "1": "1", "X": "x"},
+        ),
+        (
+            ["{tmp_path}/config1", "{tmp_path}/config2"],
+            "2b",
+            {"default": "2b", "1": "1", "2": "2b", "X": "x"},
+        ),
+        (
+            ["{tmp_path}/config2", "{tmp_path}/config1"],
+            "1",
+            {"default": "1", "1": "1", "2": "2b", "X": "x"},
+        ),
+    ],
+)
+def test_update_from_dirs(dirs, output_file_type, rootpath, tmp_path):
+    """Test `Config.update_from_dirs`."""
+    _setup_config_dirs(tmp_path)
+
+    config_dirs = []
+    for dir_ in dirs:
+        config_dirs.append(dir_.format(tmp_path=str(tmp_path)))
+    for name, path in rootpath.items():
+        path = Path(path).expanduser().absolute()
+        rootpath[name] = [path]
+
+    cfg = Config()
+    assert not cfg
+    cfg["rootpath"] = {"X": "x"}
+    cfg["search_esgf"] = "when_missing"
+
+    cfg.update_from_dirs(config_dirs)
+
+    if output_file_type is None:
+        assert "output_file_type" not in cfg
+    else:
+        assert cfg["output_file_type"] == output_file_type
+    assert cfg["rootpath"] == rootpath
+    assert cfg["search_esgf"] == "when_missing"