A memory cell with a charge trapping structure is programmed using refill cycles that include a program pulse followed by a charge balancing pulse that causes ejection of electrons from the charge trapping structure. The refill cycle causes a blue spectrum shift in the charge trap distribution in the charge trapping structure. The algorithm includes program verify operations after the program pulse, and completes when a successful program verify operation occurs after a number of refill cycles. The charge retention properties can be greatly improved by these refill cycles.