diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index c89e077..33eabea 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -4,7 +4,7 @@ ChangeLog
 8.2 (unreleased)
 ----------------
 
-- Nothing changed yet.
+- Use recursive update on grocker config
 
 
 8.1 (2024-02-23)
diff --git a/src/grocker/helpers.py b/src/grocker/helpers.py
index a6126a5..45c42df 100644
--- a/src/grocker/helpers.py
+++ b/src/grocker/helpers.py
@@ -21,6 +21,16 @@
     import importlib_resources as resources  # type: ignore
 
 
+def deep_update(initial_mapping, updating_mapping):
+    updated_mapping = initial_mapping.copy()
+    for k, v in updating_mapping.items():
+        if k in updated_mapping and isinstance(updated_mapping[k], dict) and isinstance(v, dict):
+            updated_mapping[k] = deep_update(updated_mapping[k], v)
+        else:
+            updated_mapping[k] = v
+    return updated_mapping
+
+
 def copy_resources(package, destination):
     os.makedirs(destination, exist_ok=True)
 
diff --git a/src/grocker/utils.py b/src/grocker/utils.py
index 3671785..b313a4a 100644
--- a/src/grocker/utils.py
+++ b/src/grocker/utils.py
@@ -108,11 +108,9 @@ def parse_config(config_paths, **kwargs):
 
     for config_path in config_paths:
         project_config = helpers.load_yaml(config_path)
-        config.update(project_config or {})
+        config = helpers.deep_update(config, project_config or {})
 
-    config.update({k: v for k, v in kwargs.items() if v})
-
-    return config
+    return helpers.deep_update(config, {k: v for k, v in kwargs.items() if v})
 
 
 class GrockerRequirement:
diff --git a/tests/test_config.py b/tests/test_config.py
index 0b5c4dd..29e9957 100644
--- a/tests/test_config.py
+++ b/tests/test_config.py
@@ -8,6 +8,8 @@
 import textwrap
 import unittest
 
+import yaml
+
 import grocker.builders as grocker_builders
 import grocker.utils as grocker_utils
 
@@ -25,7 +27,7 @@ def mkchtmpdir():
 
 def write_file(directory, name, content):
     with open(os.path.join(directory, name), 'w') as fp:
-        fp.write(textwrap.dedent(content))
+        fp.write(yaml.dump(yaml.safe_load(content)))
 
 
 class ConfigTestCase(unittest.TestCase):
@@ -37,11 +39,14 @@ class ConfigTestCase(unittest.TestCase):
 
     first_config_content = """
         file: first.yml
-        dependencies: first.yml
+        dependencies:
+            run: first.yml
     """[1:-1]
 
     second_config_content = """
         file: second.yml
+        dependencies:
+            build: second.yml
         runtime: second.yml
     """[1:-1]
 
@@ -54,7 +59,8 @@ def test_parse_config(self):
             config = grocker_utils.parse_config(['first.yml', 'second.yml'])
             self.assertNotIn('not_used_key', config)  # .grocker.yml is not read
             self.assertIn('entrypoint_name', config)  # grocker internal config is read
-            self.assertEqual(config.get('dependencies'), 'first.yml')  # from first.yml
+            self.assertEqual(config.get('dependencies').get('run'), 'first.yml')  # from first.yml
+            self.assertEqual(config.get('dependencies').get('build'), 'second.yml')  # from second.yml
             self.assertEqual(config.get('runtime'), 'second.yml')  # from second.yml
             self.assertEqual(config.get('file'), 'second.yml')  # from second.yml