In a control apparatus mounted in a vehicle and configured to control a power supply system, a power generation controller is configured to operate an alternator such that a charge level of a second rechargeable battery becomes a target charge level. A target charge level setter is configured to variably set the target charge level of the second rechargeable battery based on changes in a state quantity correlated with at least one of a charge state and a discharge state of the second rechargeable battery. A limiter is configured to, if there is a change in the state quantity and if a prescribed permission condition is not met, limit an operation of the alternator.