The hospital-run service will now be partly operated by a private provider, Health Intelligence.
In the future instead of diabetic patients getting their feet and eyes checked at the same time they will have to do so separately.
Andy Ennis, chief operating officer for the trust said: "It's disappointing because I think it's a step back. We had one integrated point where a diabetic person gets their eyes and feet checked at the same time.
"They tendered only for the eye service. We did lose it."
He added: "Our concern is for Bolton patients and the level of care they are going to get
"The CCG will have to commission the foot service separately."