A system for controlling a substrate temperature in a substrate processing system includes a substrate support device, a controller, a temperature sensor, and a thermal control element (TCE). The controller is configured to, during a first period, control the TCE to adjust the temperature of the substrate support device to a temperature value based on a temperature difference between the substrate temperature before the substrate is loaded onto the substrate support device and a desired temperature for the substrate support device. The temperature value is not equal to the desired temperature. The substrate is loaded onto the substrate support device after the first period begins and before the temperature of the substrate support device returns to the desired temperature. The controller is further configured to, during a second period following the first period, control the temperature of the substrate support device to the desired temperature for the substrate support device.