A system for controlling an automatic engine stop-start system of a vehicle includes a controller, an engine configured to be automatically stopped and started in response to a signal from the controller, a primary power source electrically coupled to the controller, and an auxiliary power source electrically coupled to the controller. A power control relay is electrically connected between the primary power source and the auxiliary power source and is configured to be selectively activated to isolate the auxiliary power source from the primary power source such that only the auxiliary power source is configured to supply power to the controller. The controller is configured to determine if the auxiliary power source is electrically disconnected from the vehicle when the power control relay is activated.