The shooting happened Tuesday night at an EconoLodge on Spring Street in Elizabeth.
Detectives say a man wearing a ski mask demanded the hotel's cash at gunpoint.
Some sort of struggle broke out, and the clerk was shot in the stomach and leg.
The suspect took off.
The hotel manager described the victim as a family man and loyal worker.
Police say the suspect left without any money. He also had an accomplice, who drove the getaway car.
The victim underwent surgery at University Hospital and is expected to be OK.