A maximum power point tracking charge controller for photovoltaic systems tracks the maximum power point voltage of a PV array, and employs a coupled inductor multi-phase buck converter for converting the maximum power voltage to the voltage required to charge one or more batteries. The phase configurations are phase shifted from one another. One of the phase configurations is intentionally temporarily shut down when the output power is low. A first switch or a second switch of the phase configuration that is shut down is turned on to conduct electrical current when predetermined conditions are satisfied. A method of controlling battery charging in a photovoltaic system involves operating a coupled inductor multi-phase buck converter so that one of the phase configurations is intentionally temporarily shut down when the power output is below a predetermined value.