The aim of this paper is to apply the mass integration methodology to sugarcane biorefinery using for the optimization task the flexible tolerance modified method (MFTM). The first generation plant simulated includes cleaning, milling, physical and chemical treatment, concentration, fermentation, distillation and cogeneration. The second generation plant uses the weak acid pretreatment, enzymatic hydrolysis and fermentation of sugars (pentoses and hexoses). The optimization of the source-sink superstructure was performed using the MFTM implemented in Python. It is worth pointing out that the modified flexible tolerance presented a good performance, since it found the optimum process configuration with mass integration issues attended from the current process. The results showed that mass integration methodology applied to sugarcane biorefinery was a powerful tool, since it was possible to obtain the optimized flowsheet with minimum discharge of wastes and minimum consumption of water.