diff --git a/misc/bazel/cmake/setup.cmake b/misc/bazel/cmake/setup.cmake
index 0079c480b607..fc77d6168bbe 100644
--- a/misc/bazel/cmake/setup.cmake
+++ b/misc/bazel/cmake/setup.cmake
@@ -14,6 +14,9 @@ if (NOT DEFINED CODEQL_BAZEL_WORKSPACE)
 endif ()
 
 macro(bazel)
+    message(STATUS "================================================================================")
+    message(STATUS "Running: ${BAZEL_BIN} ${BAZEL_STARTUP_OPTIONS} ${ARGN}")
+    message(STATUS "================================================================================")
     execute_process(COMMAND ${BAZEL_BIN} ${BAZEL_STARTUP_OPTIONS} ${ARGN}
             COMMAND_ERROR_IS_FATAL ANY
             OUTPUT_STRIP_TRAILING_WHITESPACE
@@ -21,6 +24,9 @@ macro(bazel)
 endmacro()
 
 macro(bazel_even_if_failing)
+    message(STATUS "================================================================================")
+    message(STATUS "Running: ${BAZEL_BIN} ${BAZEL_STARTUP_OPTIONS} ${ARGN}")
+    message(STATUS "================================================================================")
     execute_process(COMMAND ${BAZEL_BIN} ${BAZEL_STARTUP_OPTIONS} ${ARGN}
             OUTPUT_STRIP_TRAILING_WHITESPACE
             WORKING_DIRECTORY ${PROJECT_SOURCE_DIR})
@@ -46,10 +52,24 @@ macro(generate_and_include)
     string(JSON BAZEL_JSON_TARGETS GET "${BAZEL_AQUERY_RESULT}" targets)
     string(JSON LAST_IDX LENGTH "${BAZEL_JSON_TARGETS}")
     math(EXPR LAST_IDX "${LAST_IDX} - 1")
+    set(BAZEL_TARGETS_LIST "")
     foreach(IDX RANGE ${LAST_IDX})
         string(JSON CUR_BAZEL_TARGET GET "${BAZEL_JSON_TARGETS}" ${IDX} label)
         string(APPEND BAZEL_TARGETS "        '${CUR_BAZEL_TARGET}',\n")
+        list(APPEND BAZEL_TARGETS_LIST ${CUR_BAZEL_TARGET})
     endforeach ()
+    # Find and build targets that generate source files
+    if(NOT "${BAZEL_TARGETS_LIST}" STREQUAL "")
+        string(REPLACE ";" " " BAZEL_TARGETS_QUERY "${BAZEL_TARGETS_LIST}")
+        bazel_even_if_failing(cquery "filter(\"\\\\.\\(h\\|c\\|cpp\\|hpp\\)$\", kind(\"generated file\", deps(set(${BAZEL_TARGETS_QUERY}))))" --output=label OUTPUT_VARIABLE GENERATED_SOURCE_TARGETS)
+        # Build only the generator targets (strip configuration hashes)
+        if(NOT "${GENERATED_SOURCE_TARGETS}" STREQUAL "")
+            string(REGEX REPLACE " \\([^)]+\\)" "" GENERATED_SOURCE_TARGETS "${GENERATED_SOURCE_TARGETS}")
+            string(REPLACE "\n" ";" GENERATED_SOURCE_TARGETS_LIST "${GENERATED_SOURCE_TARGETS}")
+            list(REMOVE_DUPLICATES GENERATED_SOURCE_TARGETS_LIST)
+            bazel(build ${GENERATED_SOURCE_TARGETS_LIST} ${BAZEL_BUILD_OPTIONS})
+        endif()
+    endif()
     file(WRITE "${BAZEL_WORKSPACE}/.bazel-cmake/BUILD.bazel" "\
 # this file was generated by cmake
 load('@${CODEQL_BAZEL_WORKSPACE}//misc/bazel/cmake:cmake.bzl', 'generate_cmake')\n\