diff --git a/tools/FindPythonLibsNew.cmake b/tools/FindPythonLibsNew.cmake
index 014f68fb56..9948f07ac9 100644
--- a/tools/FindPythonLibsNew.cmake
+++ b/tools/FindPythonLibsNew.cmake
@@ -200,6 +200,15 @@ if(PYBIND11_PYTHONLIBS_OVERWRITE OR NOT DEFINED PYTHON_MODULE_DEBUG_POSTFIX)
 endif()
 if(PYBIND11_PYTHONLIBS_OVERWRITE OR NOT DEFINED PYTHON_MODULE_EXTENSION)
   get_filename_component(PYTHON_MODULE_EXTENSION "${_PYTHON_MODULE_EXT_SUFFIX}" EXT)
+  if (NOT "$ENV{SETUPTOOLS_EXT_SUFFIX}" STREQUAL ""
+      AND NOT "$ENV{SETUPTOOLS_EXT_SUFFIX}" STREQUAL "${PYTHON_MODULE_EXTENSION}")
+    message(AUTHOR_WARNING,
+            "SETUPTOOLS_EXT_SUFFIX is set to \"$ENV{SETUPTOOLS_EXT_SUFFIX}\", "
+            "but the auto-calculated Python extension suffix is \"${PYTHON_MODULE_EXTENSION}\". "
+            "This may cause problems when importing the Python extensions. "
+            "If you are using cross-compiling Python, you may need to "
+            "set PYTHON_MODULE_EXTENSION manually.")
+  endif()
 endif()
 
 # Make sure the Python has the same pointer-size as the chosen compiler