A control system for cost optimal operation of an energy facility including equipment covered by a maintenance contract includes equipment configured to operate during an optimization period and a controller. The controller modifies a cost function to include a maintenance cost term that defines a maintenance cost as a function of a rate variable and an equipment usage variable. The controller simulates a cost of operating the energy facility over the optimization period at each of a plurality of different values of the rate variable, selects a value of the rate variable that results in a lowest cost of operating the energy facility over the optimization period, performs an online optimization of the cost function with the rate variable set to the selected value to generate one or more setpoints for the equipment, and operates the equipment during the optimization period in accordance with the generated setpoints.