diff --git a/modules/default.nix b/modules/default.nix
index 673363c..254f66d 100644
--- a/modules/default.nix
+++ b/modules/default.nix
@@ -18,6 +18,7 @@ let
       {
         _module.args.home-manager = home-manager;
         _module.args.pkgs = mkDefault pkgs;
+        _module.args.isFlake = isFlake;
       }
       configModule
     ] ++ import ./module-list.nix { inherit pkgs isFlake; };
diff --git a/modules/module-list.nix b/modules/module-list.nix
index ef31d86..768ad0a 100644
--- a/modules/module-list.nix
+++ b/modules/module-list.nix
@@ -14,8 +14,9 @@
   ./environment/path.nix
   ./environment/session-init.nix
   ./home-manager.nix
+  ./nixpkgs/options.nix
   ./time.nix
   ./user.nix
   ./version.nix
   (pkgs.path + "/nixos/modules/misc/assertions.nix")
-] ++ pkgs.lib.optionals (!isFlake) [ ./nixpkgs.nix ]
+] ++ pkgs.lib.optionals (!isFlake) [ ./nixpkgs/config.nix ]
diff --git a/modules/nixpkgs/config.nix b/modules/nixpkgs/config.nix
new file mode 100644
index 0000000..7941b5a
--- /dev/null
+++ b/modules/nixpkgs/config.nix
@@ -0,0 +1,24 @@
+# Copyright (c) 2019-2021, see AUTHORS. Licensed under MIT License, see LICENSE.
+
+# Inspired by
+# https://github.com/rycee/home-manager/blob/master/modules/misc/nixpkgs.nix
+# (Copyright (c) 2017-2019 Robert Helgesson and Home Manager contributors,
+#  licensed under MIT License as well)
+
+{ config, lib, pkgs, ... }:
+
+with lib;
+
+{
+  ###### implementation
+
+  config = {
+
+    _module.args.pkgs = import <nixpkgs> (
+      filterAttrs (n: v: v != null) config.nixpkgs
+    );
+
+    nixpkgs.overlays = import ../../overlays;
+
+  };
+}
diff --git a/modules/nixpkgs.nix b/modules/nixpkgs/options.nix
similarity index 90%
rename from modules/nixpkgs.nix
rename to modules/nixpkgs/options.nix
index 233ec63..f23ad6c 100644
--- a/modules/nixpkgs.nix
+++ b/modules/nixpkgs/options.nix
@@ -1,11 +1,11 @@
-# Copyright (c) 2019-2020, see AUTHORS. Licensed under MIT License, see LICENSE.
+# Copyright (c) 2019-2021, see AUTHORS. Licensed under MIT License, see LICENSE.
 
 # Inspired by
 # https://github.com/rycee/home-manager/blob/master/modules/misc/nixpkgs.nix
 # (Copyright (c) 2017-2019 Robert Helgesson and Home Manager contributors,
 #  licensed under MIT License as well)
 
-{ config, lib, pkgs, ... }:
+{ config, lib, pkgs, isFlake, ... }:
 
 with lib;
 
@@ -53,11 +53,6 @@ let
     check = builtins.isFunction;
     merge = lib.mergeOneOption;
   };
-
-  _pkgs = import <nixpkgs> (
-    filterAttrs (n: v: v != null) config.nixpkgs
-  );
-
 in
 
 {
@@ -164,9 +159,13 @@ in
 
   config = {
 
-    _module.args.pkgs = _pkgs;
-
-    nixpkgs.overlays = import ../overlays;
+    assertions = [
+      {
+        assertion = isFlake -> config.nixpkgs.config == null && (config.nixpkgs.overlays == null || config.nixpkgs.overlays == []);
+        message = "In a flake setup, the options nixpkgs.* should not be used. Instead, rely on the provided flake "
+          + "outputs and pass in the necessary nixpkgs object.";
+      }
+    ];
 
   };
 }