diff --git a/src/pya/pya/pya.cc b/src/pya/pya/pya.cc
index 5f177fa56..0de6ea55c 100644
--- a/src/pya/pya/pya.cc
+++ b/src/pya/pya/pya.cc
@@ -360,6 +360,10 @@ PythonInterpreter::PythonInterpreter (bool embedded)
 
 PythonInterpreter::~PythonInterpreter ()
 {
+  for (auto m = m_modules.begin (); m != m_modules.end (); ++m) {
+    (*m)->cleanup ();
+  }
+
   m_stdout_channel = PythonRef ();
   m_stderr_channel = PythonRef ();
   m_stdout = PythonPtr ();
@@ -370,6 +374,23 @@ PythonInterpreter::~PythonInterpreter ()
   if (m_embedded) {
     Py_Finalize ();
   }
+
+  for (auto m = m_modules.begin (); m != m_modules.end (); ++m) {
+    delete *m;
+  }
+  m_modules.clear ();
+}
+
+void
+PythonInterpreter::register_module (pya::PythonModule *module)
+{
+  for (auto m = m_modules.begin (); m != m_modules.end (); ++m) {
+    if (*m == module) {
+      return; //  already registered
+    }
+  }
+
+  m_modules.push_back (module);
 }
 
 char *
diff --git a/src/pya/pya/pya.h b/src/pya/pya/pya.h
index ee8d35381..76838f4f0 100644
--- a/src/pya/pya/pya.h
+++ b/src/pya/pya/pya.h
@@ -105,6 +105,14 @@ class PYA_PUBLIC PythonInterpreter
    */
   ~PythonInterpreter ();
 
+  /**
+   *  @brief Registers a module
+   *
+   *  The registered modules are cleaned up before the interpreter shuts down. The interpreter takes
+   *  ownership of the module object.
+   */
+  void register_module (pya::PythonModule *module);
+
   /**
    *  @brief Add the given path to the search path
    */
@@ -279,7 +287,7 @@ class PYA_PUBLIC PythonInterpreter
   std::map<PyObject *, size_t> m_file_id_map;
   std::wstring mp_py3_app_name;
   bool m_embedded;
-  std::unique_ptr<pya::PythonModule> m_pya_module;
+  std::vector<pya::PythonModule *> m_modules;
 };
 
 }
diff --git a/src/pya/pya/pyaCallables.cc b/src/pya/pya/pyaCallables.cc
index 5dfc3e4f1..d12ea6905 100644
--- a/src/pya/pya/pyaCallables.cc
+++ b/src/pya/pya/pyaCallables.cc
@@ -51,6 +51,9 @@ pya_object_deallocate (PyObject *self)
   //  we better work around it.
   ++self->ob_refcnt;
 
+  //  Mute Python warnings in debug case
+  PyObject_GC_UnTrack (self);
+
   PYAObjectBase *p = PYAObjectBase::from_pyobject (self);
   p->~PYAObjectBase ();
   Py_TYPE (self)->tp_free (self);
diff --git a/src/pya/pya/pyaModule.cc b/src/pya/pya/pyaModule.cc
index 30452d669..62e6bacde 100644
--- a/src/pya/pya/pyaModule.cc
+++ b/src/pya/pya/pyaModule.cc
@@ -71,12 +71,6 @@ PythonModule::PythonModule ()
 
 PythonModule::~PythonModule ()
 {
-  PYAObjectBase::clear_callbacks_cache ();
-
-  //  the Python objects were probably deleted by Python itself as it exited -
-  //  don't try to delete them again.
-  mp_module.release ();
-
   while (!m_methods_heap.empty ()) {
     delete m_methods_heap.back ();
     m_methods_heap.pop_back ();
@@ -93,6 +87,16 @@ PythonModule::~PythonModule ()
   }
 }
 
+void
+PythonModule::cleanup ()
+{
+  //  the Python objects are probably deleted by Python itself as it exits -
+  //  don't try to delete them again in the destructor.
+  mp_module.release ();
+
+  PYAObjectBase::clear_callbacks_cache ();
+}
+
 PyObject *
 PythonModule::module ()
 {
diff --git a/src/pya/pya/pyaModule.h b/src/pya/pya/pyaModule.h
index 0adcc9586..b543ae02b 100644
--- a/src/pya/pya/pyaModule.h
+++ b/src/pya/pya/pyaModule.h
@@ -65,6 +65,12 @@ class PYA_PUBLIC PythonModule
    */
   ~PythonModule ();
 
+  /**
+   *  @brief Clean up the module
+   *  This method is called by the interpreter before Py_Finalize
+   */
+  void cleanup ();
+
   /**
    *  @brief Initializes the module
    *  This entry point is for external use where the module has not been created yet
diff --git a/src/pymod/pymodHelper.h b/src/pymod/pymodHelper.h
index 55bc56185..6d116e234 100644
--- a/src/pymod/pymodHelper.h
+++ b/src/pymod/pymodHelper.h
@@ -34,6 +34,7 @@
 
 #include "pyaModule.h"
 #include "pyaUtils.h"
+#include "pya.h"
 
 #include "gsi.h"
 #include "gsiExpression.h"
@@ -41,7 +42,12 @@
 static PyObject *
 module_init (const char *pymod_name, const char *mod_name, const char *mod_description)
 {
-  static pya::PythonModule module;
+  if (! pya::PythonInterpreter::instance ()) {
+    return 0;
+  }
+
+  pya::PythonModule *module = new pya::PythonModule ();
+  pya::PythonInterpreter::instance ()->register_module (module);
 
   PYA_TRY
   
@@ -50,10 +56,10 @@ module_init (const char *pymod_name, const char *mod_name, const char *mod_descr
     //  required for the tiling processor for example
     gsi::initialize_expressions ();
 
-    module.init (pymod_name, mod_description);
-    module.make_classes (mod_name);
+    module->init (pymod_name, mod_description);
+    module->make_classes (mod_name);
 
-    return module.take_module ();
+    return module->take_module ();
 
   PYA_CATCH_ANYWHERE