diff --git a/Configure.pl b/Configure.pl
index 83128388a3a..86b21a34812 100755
--- a/Configure.pl
+++ b/Configure.pl
@@ -72,8 +72,12 @@
     my %backends;
     if (my $nqp_bin  = $options{'with-nqp'}) {
         die "Could not find $nqp_bin" unless -e $nqp_bin;
+        my $passed_backends = $options{backends};
         $options{backends} = qx{$nqp_bin -e 'print(nqp::getcomp("nqp").backend.name)'}
             or die "Could not get backend information from $nqp_bin";
+        if (defined $options{backends} && $passed_backends ne $options{backends}) {
+            die "Passed value to --backends ($passed_backends) is overwritten by the one infered by --with-nqp ($options{backends}";
+        }
     }
     if (defined $options{backends}) {
         $options{backends} = join ",", @known_backends