A body bias is applied to a non-volatile storage system to compensate for temperature-dependent variations in threshold voltage, sub-threshold slope, depletion layer width and/or 1/f noise. A desired bias level is set based on a temperature-dependent reference signal. In one approach, a level of the biasing can decrease as temperature increases. The body bias can be applied by applying a voltage to a p-well and n-well of a substrate, applying a voltage to the p-well while grounding the n-well, or grounding the body and applying a voltage to the source and/or drain of a set of non-volatile storage elements. Further, temperature-independent and/or temperature-dependent voltages can be applied to selected and unselected word lines in the non-volatile storage system during program, read or verify operations. The temperature-dependent voltages can vary based on different temperature coefficients.