diff --git a/flake8/options/manager.py b/flake8/options/manager.py
index 3e4c128..38eb605 100644
--- a/flake8/options/manager.py
+++ b/flake8/options/manager.py
@@ -93,7 +93,7 @@ class Option(object):
             if not long_option_name:
                 raise ValueError('When specifying parse_from_config=True, '
                                  'a long_option_name must also be specified.')
-            self.config_name = self.dest
+            self.config_name = long_option_name[2:].replace('-', '_')
 
     def __repr__(self):
         return (
@@ -104,6 +104,9 @@ class Option(object):
             ).format(*self.option_args, **self.option_kwargs)
 
     def _make_dest(self, dest):
+        if dest:
+            return dest
+
         if self.long_option_name:
             return self.long_option_name[2:].replace('-', '_')
         return self.short_option_name[1]
diff --git a/tests/unit/test_option.py b/tests/unit/test_option.py
index c6fc98c..55cae5c 100644
--- a/tests/unit/test_option.py
+++ b/tests/unit/test_option.py
@@ -57,3 +57,8 @@ def test_config_name_needs_long_option_name():
     """Show that we error out if the Option should be parsed from config."""
     with pytest.raises(ValueError):
         manager.Option('-s', parse_from_config=True)
+
+
+def test_dest_is_not_overridden():
+    opt = manager.Option('-s', '--short', dest='something_not_short')
+    assert opt.dest == 'something_not_short'