diff --git a/cmake_modules/SuperBuild.cmake b/cmake_modules/SuperBuild.cmake
index 1d753cc3..fbecd086 100644
--- a/cmake_modules/SuperBuild.cmake
+++ b/cmake_modules/SuperBuild.cmake
@@ -79,6 +79,7 @@ endif(NOT WIN32)
 if (USE_PYTHON)
   find_path(PYBIND_INCLUDE_DIR pybind11/pybind11.h PATHS ${CMAKE_CURRENT_SOURCE_DIR}/external_dependencies/pybind11/include NO_DEFAULT_PATH)
     if( NOT PYBIND_INCLUDE_DIR )
+      # if the pybind submodule is missing, try to initialize and update all submodules
       execute_process(COMMAND git submodule update --init --recursive WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
         find_path(PYBIND_INCLUDE_DIR pybind11/pybind11.h ${CMAKE_CURRENT_SOURCE_DIR}/external_dependencies/pybind11/include)
     endif( NOT PYBIND_INCLUDE_DIR )
@@ -151,6 +152,23 @@ ExternalProject_Add (netgen
   STEP_TARGETS build
 )
 
+# Check if the git submodules (i.e. pybind11) are up to date
+# in case, something is wrong, emit a warning but continue
+ ExternalProject_Add_Step(netgen check_submodules
+   COMMAND cmake -P ${CMAKE_CURRENT_SOURCE_DIR}/cmake_modules/check_submodules.cmake
+   DEPENDERS install # Steps on which this step depends
+   )
+
+# Due to 'ALWAYS 1', this step is always run which also forces a build of
+# the Netgen subproject
+ ExternalProject_Add_Step(netgen check_submodules1
+   COMMAND cmake -P ${CMAKE_CURRENT_SOURCE_DIR}/cmake_modules/check_submodules.cmake
+   DEPENDEES configure # Steps on which this step depends
+   DEPENDERS build     # Steps that depend on this step
+   ALWAYS 1            # No stamp file, step always runs
+   )
+
+
 install(CODE "execute_process(COMMAND cmake --build . --target install --config ${CMAKE_BUILD_TYPE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/netgen)")
 
 add_custom_target(test_netgen
diff --git a/cmake_modules/check_submodules.cmake b/cmake_modules/check_submodules.cmake
new file mode 100644
index 00000000..f49923fa
--- /dev/null
+++ b/cmake_modules/check_submodules.cmake
@@ -0,0 +1,13 @@
+execute_process(COMMAND git submodule status --recursive WORKING_DIRECTORY "${CMAKE_CURRENT_LIST_DIR}/../" OUTPUT_VARIABLE git_status_output)
+string(REPLACE "\n" ";" git_status_output "${git_status_output}")
+foreach( a ${git_status_output})
+  if(NOT ${a} MATCHES " [a-f,0-9]* external_dependencies[.]*")
+    message(WARNING
+"*****************************************************************
+      WARNING: The git submodules are out of sync! Please run
+      git submodule update --init --recursive
+      in your source directory
+*****************************************************************")
+  endif()
+endforeach()
+