diff --git a/mypy/main.py b/mypy/main.py
index 6824bdd29df7..27d7bf461021 100644
--- a/mypy/main.py
+++ b/mypy/main.py
@@ -277,27 +277,31 @@ def infer_python_version_and_executable(options: Options,
     This function mutates options based on special_opts to infer the correct Python version and
     executable to use.
     """
+    # Check Options in case python_version is set in a config file, but prefer command
+    # line arguments.
+    python_version = special_opts.python_version or options.python_version
+
     # Infer Python version and/or executable if one is not given
 
     # TODO: (ethanhs) Look at folding these checks and the site packages subprocess calls into
     # one subprocess call for speed.
-    if special_opts.python_executable is not None and special_opts.python_version is not None:
+    if special_opts.python_executable is not None and python_version is not None:
         py_exe_ver = _python_version_from_executable(special_opts.python_executable)
-        if py_exe_ver != special_opts.python_version:
+        if py_exe_ver != python_version:
             raise PythonExecutableInferenceError(
                 'Python version {} did not match executable {}, got version {}.'.format(
-                    special_opts.python_version, special_opts.python_executable, py_exe_ver
+                    python_version, special_opts.python_executable, py_exe_ver
                 ))
         else:
-            options.python_version = special_opts.python_version
+            options.python_version = python_version
             options.python_executable = special_opts.python_executable
-    elif special_opts.python_executable is None and special_opts.python_version is not None:
-        options.python_version = special_opts.python_version
+    elif special_opts.python_executable is None and python_version is not None:
+        options.python_version = python_version
         py_exe = None
         if not special_opts.no_executable:
-            py_exe = _python_executable_from_version(special_opts.python_version)
+            py_exe = _python_executable_from_version(python_version)
         options.python_executable = py_exe
-    elif special_opts.python_version is None and special_opts.python_executable is not None:
+    elif python_version is None and special_opts.python_executable is not None:
         options.python_version = _python_version_from_executable(
             special_opts.python_executable)
         options.python_executable = special_opts.python_executable
@@ -454,7 +458,7 @@ def add_invertible_flag(flag: str,
         help='Type check code assuming it will be running on Python x.y',
         dest='special-opts:python_version')
     platform_group.add_argument(
-        '-2', '--py2', dest='python_version', action='store_const',
+        '-2', '--py2', dest='special-opts:python_version', action='store_const',
         const=defaults.PYTHON2_VERSION,
         help="Use Python 2 mode (same as --python-version 2.7)")
     platform_group.add_argument(
diff --git a/mypy/test/testargs.py b/mypy/test/testargs.py
index bccbafaf4c8b..175e3e46c300 100644
--- a/mypy/test/testargs.py
+++ b/mypy/test/testargs.py
@@ -60,6 +60,20 @@ def test_executable_inference(self) -> None:
         assert str(e.value) == 'Python version (2, 10) did not match executable {}, got' \
                                ' version {}.'.format(sys.executable, sys.version_info[:2])
 
+        # If a configuration file specifies python_version, it will be set on options.
+        # Use that to figure out how to determine a value for python_executable, when
+        # special_opts.python_version is None.
+        special_opts = argparse.Namespace()
+        special_opts.python_executable = None
+        special_opts.python_version = None
+        special_opts.no_executable = None
+        options = Options()
+        options.python_executable = None
+        options.python_version = sys.version_info[:2]
+        infer_python_version_and_executable(options, special_opts)
+        assert options.python_version == sys.version_info[:2]
+        assert options.python_executable == sys.executable
+
         # test that --no-site-packages will disable executable inference
         matching_version = base + ['--python-version={}'.format(sys_ver_str),
                                    '--no-site-packages']