Yes, there is secure parking, which was very important to us as we had a large truck full of personal possessions for moving house. There was no problem.
They have a 4 Level parking garage on the property. I did not use it so I'm not sure if they have security in the garage. You do have to get a ticket and pass through a automated gate when entering the property, all vehicles including taxis must dos this. The property is in a wonderful location and I always felt secure. The grounds are beautiful and well manicured.
Get an answer from Holiday Inn Queretaro Centro Historico staff and past guests.