diff --git a/nixos/modules/system/activation/activation-script.nix b/nixos/modules/system/activation/activation-script.nix
index 4986a8bf0519..d26e41294d11 100644
--- a/nixos/modules/system/activation/activation-script.nix
+++ b/nixos/modules/system/activation/activation-script.nix
@@ -260,7 +260,8 @@ in
       ''
       else ''
         rm -f /usr/bin/env
-        rmdir --ignore-fail-on-non-empty /usr/bin /usr
+        if test -d /usr/bin; then rmdir --ignore-fail-on-non-empty /usr/bin; fi
+        if test -d /usr; then rmdir --ignore-fail-on-non-empty /usr; fi
       '';
 
     system.activationScripts.specialfs =