Apparatus and methods of substrate temperature control during thin film solar cell manufacturing are provided. One method comprises performing a temperature stabilization process on a substrate to pre-heat the substrate for a time period in a first chamber, calculating a wait time period for a second chamber, wherein the wait time period is bases on the availability of the second chamber, the availability of a vacuum transfer robot adapted to transfer the substrate from the first chamber to the second chamber, or both, and adjusting the temperature stabilization time period to compensate for the loss of heat from the substrate during the wait time period.