diff --git a/tools/FindPythonLibsNew.cmake b/tools/FindPythonLibsNew.cmake
index 014f68fb5..7351bcaa6 100644
--- a/tools/FindPythonLibsNew.cmake
+++ b/tools/FindPythonLibsNew.cmake
@@ -200,6 +200,16 @@ 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
diff --git a/tools/pybind11NewTools.cmake b/tools/pybind11NewTools.cmake
index 6bd6ca2be..087784c22 100644
--- a/tools/pybind11NewTools.cmake
+++ b/tools/pybind11NewTools.cmake
@@ -171,6 +171,16 @@ if(NOT _PYBIND11_CROSSCOMPILING)
       set(PYTHON_MODULE_EXTENSION
           "${_PYTHON_MODULE_EXTENSION}"
           CACHE INTERNAL "")
+      if((NOT "$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()
   endif()
 else()