diff --git a/doit/doit_cmd.py b/doit/doit_cmd.py
index 5c9d143d..9ffe33ea 100644
--- a/doit/doit_cmd.py
+++ b/doit/doit_cmd.py
@@ -52,14 +52,20 @@ class DoitConfig():
     _TOML_LIBS = ['toml', 'tomlkit']
     PLUGIN_TYPES = ['command', 'loader', 'backend', 'reporter']
 
-    def __init__(self):
+    def __init__(self, application_name):
         self._toml = None
         self.config = defaultdict(dict)
+        self._application_name = application_name
 
-    def loads(self, config_filenames):
+    def loads(self, config_filenames, toml_config_files_prefix):
         for config_filename in config_filenames:
             if str(config_filename).lower().endswith('.toml'):
-                prefix = 'tool.doit' if config_filename == 'pyproject.toml' else ''
+                if toml_config_files_prefix:
+                    prefix = toml_config_files_prefix
+                elif config_filename == 'pyproject.toml':
+                    prefix = f'tool.{self._application_name}'
+                else:
+                    prefix = ''
                 toml_config = self.load_config_toml(config_filename, prefix)
                 for section in toml_config:
                     self.config[section].update(toml_config[section].items())
@@ -159,7 +165,9 @@ class DoitMain(object):
 
     def __init__(self, task_loader=None,
                  config_filenames=('pyproject.toml', 'doit.cfg'),
-                 extra_config=None):
+                 extra_config=None,
+                 application_name='doit',
+                 toml_config_files_prefix=None):
         """
         :param extra_config: dict of extra argument values (by argument name)
                              This is parameter is only used by explicit API call.
@@ -179,8 +187,8 @@ def __init__(self, task_loader=None,
                 self.config[section].update(items)
 
         # combine config option from INI/TOML files and API
-        config_in = DoitConfig()
-        config_in.loads(config_filenames)
+        config_in = DoitConfig(application_name)
+        config_in.loads(config_filenames, toml_config_files_prefix=toml_config_files_prefix)
         for section, vals in config_in.as_dict().items():
             self.config[section].update(vals)
 
diff --git a/tests/sample_with_prefix.toml b/tests/sample_with_prefix.toml
new file mode 100644
index 00000000..c28a87b3
--- /dev/null
+++ b/tests/sample_with_prefix.toml
@@ -0,0 +1,12 @@
+[tool.doit]
+optx = "6"
+opty = "7"
+
+[tool.doit.plugins.command]
+foo = "tests.sample_plugin:MyCmd"
+
+[tool.doit.commands.foo]
+nval = 33
+
+[tool.doit.tasks.bar]
+opt = "baz"
diff --git a/tests/test_doit_cmd.py b/tests/test_doit_cmd.py
index e9c8323e..55f53500 100644
--- a/tests/test_doit_cmd.py
+++ b/tests/test_doit_cmd.py
@@ -178,6 +178,19 @@ def test_merge_api_toml_config(self):
         assert main.config['foo'] == {'nval': 33}
         assert main.config['task:bar'] == {'opt': "baz"}
 
+    def test_merge_api_toml_config_with_prefix(self):
+        config_filename = os.path.join(os.path.dirname(__file__), 'sample_with_prefix.toml')
+        main = doit_cmd.DoitMain(config_filenames=config_filename,
+                                 toml_config_files_prefix="tool.doit")
+        assert 1 == len(main.config['COMMAND'])
+        # test loaded plugin command is actually used with plugin name
+        assert 'foo' in main.get_cmds()
+        # INI has higher preference the api_config
+        assert main.config['GLOBAL'] == {'optx':'6', 'opty':'7'}
+
+        assert main.config['foo'] == {'nval': 33}
+        assert main.config['task:bar'] == {'opt': "baz"}
+
 
     def test_find_pyproject_toml_config(self):
         config_filename = os.path.join(os.path.dirname(__file__), 'pyproject.toml')