A programming technique which reduces program disturb in a non-volatile storage system is disclosed. A positive voltage may be applied to a substrate (e.g., p-well) during programming. Biasing the substrate may improve boosting of channels of unselected NAND strings, which may reduce program disturb. The substrate may be charged up during the programming operation, and discharged after programming. Therefore, for operations such as verify and read, the substrate may be grounded. In one embodiment, the substrate is charged just prior to applying a program pulse, then discharged prior to a program verify operation. In one embodiment, the substrate is charged while unselected word lines are ramped up to a pass voltage. The substrate bias may depend on program voltage, temperature, and/or hot count.