--- a/setupext.py
+++ b/setupext.py
@@ -19,6 +19,7 @@
 
 _log = logging.getLogger(__name__)
 
+MSYS = "MSYSTEM" in os.environ
 
 def _get_xdg_cache_dir():
     """
@@ -198,10 +199,10 @@
     'backend': config.get('rc_options', 'backend', fallback=None),
     'system_freetype': config.getboolean(
         'libs', 'system_freetype',
-        fallback=sys.platform.startswith(('aix', 'os400'))
+        fallback=sys.platform.startswith(('aix', 'os400')) or MSYS
     ),
     'system_qhull': config.getboolean(
-        'libs', 'system_qhull', fallback=sys.platform.startswith('os400')
+        'libs', 'system_qhull', fallback=sys.platform.startswith('os400') or MSYS
     ),
 }
 
@@ -225,7 +226,7 @@
     """
     Get path to pkg-config and set up the PKG_CONFIG environment variable.
     """
-    if sys.platform == 'win32':
+    if sys.platform == 'win32' and not MSYS:
         return None
     pkg_config = os.environ.get('PKG_CONFIG') or 'pkg-config'
     if shutil.which(pkg_config) is None:
@@ -277,7 +278,7 @@
 
     # conda Windows header and library paths.
     # https://github.com/conda/conda/issues/2312 re: getting the env dir.
-    if sys.platform == 'win32':
+    if sys.platform == 'win32' and not MSYS:
         conda_env_path = (os.getenv('CONDA_PREFIX')  # conda >= 4.1
                           or os.getenv('CONDA_DEFAULT_ENV'))  # conda < 4.1
         if conda_env_path and os.path.isdir(conda_env_path):