diff --git a/programs/test/CMakeLists.txt b/programs/test/CMakeLists.txt
index 949708420c..ca6e8b2070 100644
--- a/programs/test/CMakeLists.txt
+++ b/programs/test/CMakeLists.txt
@@ -56,6 +56,7 @@ if(GEN_FILES)
                 ${CMAKE_CURRENT_SOURCE_DIR}/../../tf-psa-crypto/include/psa/crypto_config.h
                 ${CMAKE_CURRENT_SOURCE_DIR}/../../scripts/data_files/query_config.fmt
                 ${CMAKE_CURRENT_BINARY_DIR}/query_config.c
+        WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/../..
         DEPENDS
             ${CMAKE_CURRENT_SOURCE_DIR}/../../scripts/generate_query_config.pl
             ${CMAKE_CURRENT_SOURCE_DIR}/../../include/mbedtls/mbedtls_config.h
diff --git a/scripts/generate_query_config.pl b/scripts/generate_query_config.pl
index 61ea9028a4..e99d633de6 100755
--- a/scripts/generate_query_config.pl
+++ b/scripts/generate_query_config.pl
@@ -49,6 +49,8 @@ if( @ARGV ) {
           or die "No arguments supplied, must be run from project root or a first-level subdirectory\n";
     }
 }
+-f 'include/mbedtls/build_info.h'
+  or die "$0: must be run from project root, or from a first-level subdirectory with no arguments\n";
 
 # Excluded macros from the generated query_config.c. For example, macros that
 # have commas or function-like macros cannot be transformed into strings easily