diff --git a/docs/changelog/1535.bugfix.rst b/docs/changelog/1535.bugfix.rst
new file mode 100644
index 000000000..340cd04a2
--- /dev/null
+++ b/docs/changelog/1535.bugfix.rst
@@ -0,0 +1,2 @@
+Stable order within ``pyenv.cfg`` and add ``include-system-site-packages`` only for creators that reference a global
+Python - by ``gaborbernat``.
diff --git a/src/virtualenv/create/creator.py b/src/virtualenv/create/creator.py
index a402fdfcc..11e0debbc 100644
--- a/src/virtualenv/create/creator.py
+++ b/src/virtualenv/create/creator.py
@@ -32,7 +32,6 @@ def __init__(self, options, interpreter):
         self.interpreter = interpreter
         self._debug = None
         self.dest = Path(options.dest)
-        self.enable_system_site_package = options.system_site
         self.clear = options.clear
         self.pyenv_cfg = PyEnvCfg.from_folder(self.dest)
 
@@ -45,7 +44,6 @@ def __unicode__(self):
     def _args(self):
         return [
             ("dest", six.ensure_text(str(self.dest))),
-            ("global", self.enable_system_site_package),
             ("clear", self.clear),
         ]
 
@@ -58,16 +56,9 @@ def add_parser_arguments(cls, parser, interpreter, meta):
             "--clear",
             dest="clear",
             action="store_true",
-            help="clear out the non-root install and start from scratch",
+            help="remove the destination directory if exist before starting (will overwrite files otherwise)",
             default=False,
         )
-        parser.add_argument(
-            "--system-site-packages",
-            default=False,
-            action="store_true",
-            dest="system_site",
-            help="give the virtual environment access to the system site-packages dir",
-        )
 
     @classmethod
     def validate_dest(cls, raw_value):
@@ -151,13 +142,11 @@ def can_create(cls, interpreter):
         return True
 
     def set_pyenv_cfg(self):
-        self.pyenv_cfg.content = {
-            "home": self.interpreter.system_exec_prefix,
-            "include-system-site-packages": "true" if self.enable_system_site_package else "false",
-            "implementation": self.interpreter.implementation,
-            "version_info": ".".join(str(i) for i in self.interpreter.version_info),
-            "virtualenv": __version__,
-        }
+        self.pyenv_cfg.content = OrderedDict()
+        self.pyenv_cfg["home"] = self.interpreter.system_exec_prefix
+        self.pyenv_cfg["implementation"] = self.interpreter.implementation
+        self.pyenv_cfg["version_info"] = ".".join(str(i) for i in self.interpreter.version_info)
+        self.pyenv_cfg["virtualenv"] = __version__
 
     @property
     def debug(self):
diff --git a/src/virtualenv/create/via_global_ref/api.py b/src/virtualenv/create/via_global_ref/api.py
index cbb55a41e..1fc9999a4 100644
--- a/src/virtualenv/create/via_global_ref/api.py
+++ b/src/virtualenv/create/via_global_ref/api.py
@@ -12,10 +12,18 @@ class ViaGlobalRefApi(Creator):
     def __init__(self, options, interpreter):
         super(ViaGlobalRefApi, self).__init__(options, interpreter)
         self.symlinks = getattr(options, "copies", False) is False
+        self.enable_system_site_package = options.system_site
 
     @classmethod
     def add_parser_arguments(cls, parser, interpreter, meta):
         super(ViaGlobalRefApi, cls).add_parser_arguments(parser, interpreter, meta)
+        parser.add_argument(
+            "--system-site-packages",
+            default=False,
+            action="store_true",
+            dest="system_site",
+            help="give the virtual environment access to the system site-packages dir",
+        )
         group = parser.add_mutually_exclusive_group()
         if meta.can_symlink:
             group.add_argument(
@@ -34,3 +42,10 @@ def add_parser_arguments(cls, parser, interpreter, meta):
                 dest="copies",
                 help="try to use copies rather than symlinks, even when symlinks are the default for the platform",
             )
+
+    def _args(self):
+        return super(ViaGlobalRefApi, self)._args() + [("global", self.enable_system_site_package)]
+
+    def set_pyenv_cfg(self):
+        super(ViaGlobalRefApi, self).set_pyenv_cfg()
+        self.pyenv_cfg["include-system-site-packages"] = "true" if self.enable_system_site_package else "false"
diff --git a/src/virtualenv/pyenv_cfg.py b/src/virtualenv/pyenv_cfg.py
index 923316b8b..8388208ae 100644
--- a/src/virtualenv/pyenv_cfg.py
+++ b/src/virtualenv/pyenv_cfg.py
@@ -1,6 +1,7 @@
 from __future__ import absolute_import, unicode_literals
 
 import logging
+from collections import OrderedDict
 
 import six
 
@@ -16,12 +17,12 @@ def from_folder(cls, folder):
 
     @classmethod
     def from_file(cls, path):
-        content = cls._read_values(path) if path.exists() else {}
+        content = cls._read_values(path) if path.exists() else OrderedDict()
         return PyEnvCfg(content, path)
 
     @staticmethod
     def _read_values(path):
-        content = {}
+        content = OrderedDict()
         for line in path.read_text(encoding="utf-8").splitlines():
             equals_at = line.index("=")
             key = line[:equals_at].strip()