diff --git a/CMakeLists.txt b/CMakeLists.txt
index b9d98bd4f52..5cba6ee3a8b 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -131,6 +131,17 @@ foreach(optional_include_dir
   endif()
 endforeach()
 
+# Don't inherit compiler flags from the environment
+foreach(var AFLAGS CFLAGS CXXFLAGS CPPFLAGS LDFLAGS)
+  if(DEFINED ENV{${var}})
+    message(WARNING "The environment variable '${var}' was set to $ENV{${var}}, "
+                    "but Zephyr ignores flags from the environment. Use 'cmake "
+                    "-DEXTRA_${var}=$ENV{${var}}' instead."
+    )
+    unset(ENV{${var}})
+  endif()
+endforeach()
+
 zephyr_compile_definitions(
   KERNEL
   __ZEPHYR__=1
diff --git a/cmake/modules/generic_toolchain.cmake b/cmake/modules/generic_toolchain.cmake
index 15697517f68..821213e6d99 100644
--- a/cmake/modules/generic_toolchain.cmake
+++ b/cmake/modules/generic_toolchain.cmake
@@ -20,15 +20,6 @@ if(NOT TOOLCHAIN_ROOT)
 endif()
 zephyr_file(APPLICATION_ROOT TOOLCHAIN_ROOT)
 
-# Don't inherit compiler flags from the environment
-foreach(var AFLAGS CFLAGS CXXFLAGS CPPFLAGS LDFLAGS)
-  if(DEFINED ENV{${var}})
-    message(WARNING "The environment variable '${var}' was set to $ENV{${var}},
-but Zephyr ignores flags from the environment. Use 'cmake -DEXTRA_${var}=$ENV{${var}}' instead.")
-    unset(ENV{${var}})
-  endif()
-endforeach()
-
 # Host-tools don't unconditionally set TOOLCHAIN_HOME anymore,
 # but in case Zephyr's SDK toolchain is used, set TOOLCHAIN_HOME
 if("${ZEPHYR_TOOLCHAIN_VARIANT}" STREQUAL "zephyr")