diff --git a/guix/build/gnu-build-system.scm b/guix/build/gnu-build-system.scm
index 5f08b9d6ac..f9e6f5013d 100644
--- a/guix/build/gnu-build-system.scm
+++ b/guix/build/gnu-build-system.scm
@@ -72,7 +72,9 @@ (define* (set-paths #:key target inputs native-inputs
                     (search-paths '()) (native-search-paths '())
                     #:allow-other-keys)
   (define input-directories
-    (match inputs
+    ;; The "source" input can be a directory, but we don't want it for search
+    ;; paths.  See <https://issues.guix.gnu.org/44924>.
+    (match (alist-delete "source" inputs)
       (((_ . dir) ...)
        dir)))