An apparatus and method for controlling an application of power to power a plasma chamber. A detector detects actual power out from the power stage to the plasma chamber during a sampling interval. A compare module compares the actual power out during the sampling interval to a present power setting during the sampling interval and generates a compensation value. An adjust module updates the present power setting for the power stage with the compensation value to provide a new power setting for the power stage to control the power out from power stage to the plasma chamber during the deposition process whereby power losses occurring during the deposition process are compensated during the deposition process. If there is a fixed time period for the deposition process, the compensation method and apparatus may be used to compensate the deposition process for energy losses without extending the duration of the deposition process.