The combined use of Advanced Oxidation Processes (AOP) and conventional bio-processes has been suggested for the efficient treatment of wastewaters with a significant presence of recalcitrant contaminants. However, no models have been proposed to describe such combined processes, which prevents further design and operational optimization. Thus, by combining models previously reported this work contributes a first model integrating AOPs and bio-processes. Mass balances were reformulated by consistently linking the variables used in each model. The model was implemented using Simulink® and it was tested and analyzed using several process configurations (photo-Fenton processes followed by a biological treatment as well as a biological treatment followed by a photo-Fenton process). The outlet concentrations of total organic carbon (TOC) and substrate (S) were monitored for various wastewater compositions, which allowed analyzing the performance of the integrated system and suggesting suitable treatment arrangements. Different treatment options were discussed and the capability of the integrated bio/AOP and AOP/bio models was shown to allow a systematic approach to design, operation, and control of integrated wastewater treatment plants in the future. Further research will be oriented to improve the understanding of the potential key parameters as well as their inclusion in the model.