diff --git a/IPython/config/loader.py b/IPython/config/loader.py
index 196ed49..e57cc7e 100644
--- a/IPython/config/loader.py
+++ b/IPython/config/loader.py
@@ -233,13 +233,26 @@ class Config(dict):
     
     def copy(self):
         return type(self)(dict.copy(self))
+        # copy nested config objects
+        for k, v in self.items():
+            if isinstance(v, Config):
+                new_config[k] = v.copy()
+        return new_config
 
     def __copy__(self):
         return self.copy()
 
     def __deepcopy__(self, memo):
-        import copy
-        return type(self)(copy.deepcopy(list(self.items())))
+        new_config = type(self)()
+        for key, value in self.items():
+            if isinstance(value, (Config, LazyConfigValue)):
+                # deep copy config objects
+                value = copy.deepcopy(value, memo)
+            elif type(value) in {dict, list, set, tuple}:
+                # shallow copy plain container traits
+                value = copy.copy(value)
+            new_config[key] = value
+        return new_config
     
     def __getitem__(self, key):
         try:
diff --git a/IPython/config/tests/test_loader.py b/IPython/config/tests/test_loader.py
index dc8f257..0cb575e 100644
--- a/IPython/config/tests/test_loader.py
+++ b/IPython/config/tests/test_loader.py
@@ -4,6 +4,8 @@
 # Copyright (c) IPython Development Team.
 # Distributed under the terms of the Modified BSD License.
 
+import copy
+import logging
 import os
 import pickle
 import sys
@@ -319,11 +321,15 @@ class TestConfig(TestCase):
         c1.Foo.bam = 30
         c1.a = 'asdf'
         c1.b = range(10)
-        import copy
+        c1.Test.logger = logging.Logger('test')
+        c1.Test.get_logger = logging.getLogger('test')
         c2 = copy.deepcopy(c1)
         self.assertEqual(c1, c2)
         self.assertTrue(c1 is not c2)
         self.assertTrue(c1.Foo is not c2.Foo)
+        self.assertTrue(c1.Test is not c2.Test)
+        self.assertTrue(c1.Test.logger is c2.Test.logger)
+        self.assertTrue(c1.Test.get_logger is c2.Test.get_logger)
 
     def test_builtin(self):
         c1 = Config()