Experimental tests were performed to evaluate the effect of intense pulsed light (IPL) treatment on microbial inactivation of yeast cell suspensions of Saccharomyces cerevisiae CBS 493.94 and Candida utilis MIUG 3.5. Regression analysis of microbial inactivation with IPL was then investigated. The aim of this study was to apply the response surface methodology (RSM) to define the relationship between the reduction of yeast cells and the process parameters, namely energetic density of light and duration of IPL treatment. Moreover, RSM was used to verify the predicted models and to adapt them on particular conditions of yeast cells inactivation by IPL treatment. The final model shows the dependency of the yeast cells reduction by independent variables (energetic density of light and duration of IPL treatment) and certain binary interactions of the IPL process parameters. The response surface follows the reduction of yeast cells and reaches the lowest level for N/No = 0. This level represents the optimal area of the response surface, which is ideal for any microbial inactivation treatment.