diff --git a/app/keymap-module/modules/modules.cmake b/app/keymap-module/modules/modules.cmake
index f513bcc4f5..6aa6288510 100644
--- a/app/keymap-module/modules/modules.cmake
+++ b/app/keymap-module/modules/modules.cmake
@@ -50,10 +50,12 @@ if (ZMK_CONFIG)
     set(ENV{ZMK_CONFIG} "${ZMK_CONFIG}")
     if(EXISTS ${ZMK_CONFIG}/boards)
         message(STATUS "Adding ZMK config directory as board root: ${ZMK_CONFIG}")
+        message(DEPRECATION "The `config/boards` folder is deprecated. Please use a module instead. See https://zmk.dev/docs/development/hardware-integration/new-shield and https://zmk.dev/docs/development/module-creation for more information.")
         list(APPEND BOARD_ROOT ${ZMK_CONFIG})
     endif()
     if(EXISTS ${ZMK_CONFIG}/dts)
         message(STATUS "Adding ZMK config directory as DTS root: ${ZMK_CONFIG}")
+        message(DEPRECATION "The `config/dts` folder is deprecated. Please use a module instead. See https://zmk.dev/docs/development/hardware-integration/new-shield and https://zmk.dev/docs/development/module-creation for more information.")
         list(APPEND DTS_ROOT ${ZMK_CONFIG})
     endif()
 endif()