Spent mushroom substrate (SMS) is defined as the biomass waste generated during industrial mushroom cultivation. Utilization of SMS has been extensively researched and has immense potential as a sustainable substrate for generating biogas that can offset fossil fuel use. This closed loop energy generation process that can be set up in mushroom plants will reduce the dependence on fossil fuels and has the potential to reduce greenhouse gas emissions, which will benefit the environment. Anaerobic co-digestion of SMS with different agricultural wastes such as livestock manure would result in enhanced biogas production. In this study, the anaerobic co-digestion of SMS was carried out by combing yellow back fungus SMS along with chicken, dairy and pig manure. SMS combined with chicken manure yielded a slightly higher cumulative methane yield when compared with the combination of dairy manure and pig manure. Factors such as the total solids (TS) and the relative ratio of manure to SMS loading had a significant impact on the cumulative methane yield, volatile solids removal, with a particularly prominent synergistic effect. The synergistic effect was also closely related to the C/N ratio, and under experimental conditions (TS = 15%, SMS relative ratio of 50% and C/N ratio = 25.6), the cumulative methane yield of SMS with chicken manure (CM) was increased by 414% compared with that obtained using SMS or CM separately. We carried out a multiple linear regression (MLR) analysis, a statistical technique that uses several explanatory variables to predict the outcome of a response variable. Our analysis concluded that by using operating conditions (TS = 15%, and SMS ratio = 38.9), we were able to achieve the maximum cumulative methane yield (CMY).