diff --git a/scripts/generate_query_config.pl b/scripts/generate_query_config.pl
index 49e363de54..99128ca7ac 100755
--- a/scripts/generate_query_config.pl
+++ b/scripts/generate_query_config.pl
@@ -122,6 +122,7 @@ for my $root (@header_roots) {
     # Exclude some headers that are included by build_info.h and cannot
     # be included directly.
     push @header_files, grep {!m[
+            ^psa/crypto_(platform|struct)\.h$ | # have alt versions, included by psa/crypto.h anyway
             ^mbedtls/platform_time\.h$ | # errors without time.h
             _config\.h |
             [/_]adjust[/_]