diff --git a/cmake/QtProcessConfigureArgs.cmake b/cmake/QtProcessConfigureArgs.cmake
index 9b9c105d58a..33967313568 100644
--- a/cmake/QtProcessConfigureArgs.cmake
+++ b/cmake/QtProcessConfigureArgs.cmake
@@ -34,11 +34,9 @@ function(is_non_empty_valid_arg arg value)
     endif()
 endfunction()
 
-function(error_in_per_repo_build arg)
+function(warn_in_per_repo_build arg)
     if(NOT TOP_LEVEL)
-        message(FATAL_ERROR
-            "Using option '${arg}' is not allowed in a per-repo build, it only "
-            "works in a top-level build.")
+        message(WARNING "Command line option ${arg} is only effective in top-level builds")
     endif()
 endfunction()
 
@@ -93,7 +91,7 @@ while(NOT "${configure_args}" STREQUAL "")
     elseif(arg STREQUAL "-write-options-for-conan")
         list(POP_FRONT configure_args options_json_file)
     elseif(arg STREQUAL "-skip")
-        error_in_per_repo_build("${arg}")
+        warn_in_per_repo_build("${arg}")
         list(POP_FRONT configure_args qtrepos)
         is_non_empty_valid_arg("${arg}" "${qtrepos}")
         list(TRANSFORM qtrepos REPLACE "," ";")
@@ -101,7 +99,7 @@ while(NOT "${configure_args}" STREQUAL "")
             push("-DBUILD_${qtrepo}=OFF")
         endforeach()
     elseif(arg STREQUAL "-submodules")
-        error_in_per_repo_build("${arg}")
+        warn_in_per_repo_build("${arg}")
         list(POP_FRONT configure_args submodules)
         is_non_empty_valid_arg("${arg}" "${submodules}")
         list(TRANSFORM submodules REPLACE "," "[[;]]")