Surface treatment optimization requires the control of the ion dose and the workpiece temperature, two parameters that are not trivially measurable in plasma-based ion implantation. A temperature and ion fluence monitoring system has been developed and implemented in a plasma-based ion implanter. It is based on the measurement with a thermopile of the radiation emitted from the back face of a thin copper disk inserted in the stainless steel sample holder. Since the incident ions carry practically all the incident power, the measurement of the Cu disk temperature that increases during implantation can provide an evaluation of the ion fluence in real time. A model has been developed for the deconvolution of the temperature data and has been fitted to the temperature behavior during implantation. A good agreement between the total integrated doses, evaluated with Rutherford backscattering spectroscopy characterization, and the ion fluence calculated by means of this model has been obtained with a discrepancy less than 16%.