diff --git a/guix/lint.scm b/guix/lint.scm
index 72582cfffb..bda5c0cd77 100644
--- a/guix/lint.scm
+++ b/guix/lint.scm
@@ -7,7 +7,7 @@
 ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
 ;;; Copyright © 2017 Alex Kost <alezost@gmail.com>
 ;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
-;;; Copyright © 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2017, 2018, 2020 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2018, 2019 Arun Isaac <arunisaac@systemreboot.net>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -286,7 +286,8 @@ (define (package-input-intersection inputs-to-check input-names)
 (define (check-inputs-should-be-native package)
   ;; Emit a warning if some inputs of PACKAGE are likely to belong to its
   ;; native inputs.
-  (let ((inputs (package-inputs package))
+  (let ((inputs (append (package-inputs package)
+                        (package-propagated-inputs package)))
         (input-names
          '("pkg-config"
             "autoconf"