Você pode substituir o método save.
class MyModel(mongoengine.Document):
creation_date = mongo.DateTimeField()
modified_date = mongo.DateTimeField(default=datetime.datetime.now)
def save(self, *args, **kwargs):
if not self.creation_date:
self.creation_date = datetime.datetime.now()
self.modified_date = datetime.datetime.now()
return super(MyModel, self).save(*args, **kwargs)