In recent years, bioderived ionic liquids have gained attention as a new promising approach for lignocellulosic biomass pretreatment. In this work, Agave tequilana bagasse (ATB), an attractive bioenergy feedstock in Mexico, was pretreated with a bioderived ionic liquid (cholinium lysinate) for the first time. Optimization of the pretreatment conditions, in-depth biomass characterization and methane generation via anaerobic digestion are the main contributions of this work. The results indicated optimized pretreatment conditions of 124 °C, 205 min and 20% solids loading by applying a central composite design. The optimized pretreated ATB was able to produce an elevated sugar yield of 51.4 g total sugars per g ATB due to their high delignification (45.4%) and changes in their chemical linkages although an increase in cellulose crystallinity was found (0.51 untreated vs. 0.62 pretreated). Finally, the mass balance showed that 38.2 kg glucose and 13.1 kg xylose were converted into 12.5 kg of methane per 100 kg of untreated ATB, representing 86% of the theoretical methane yield and evidencing the potential of this biorefinery scheme.