Occurrence of calcium oxalate (CaC2O4 - CaOX) crystals has been observed in more than 215 plant families. However, very little is known about the effects of calcium oxalate on biomass pretreatment and saccharification. Agave bagasse (AGB) was used as a model material due to its natural high levels of CaOX. To understand the physicochemical changes in function of biomass pretreatment, both raw AGB and CaOX-extracted agave bagasse (EAB) were subjected to ionic liquid (IL) with 1-Butyl-3-methylimidazolium chloride [C(4)C(1)Im][Cl] and alkaline hydrogen peroxide (AHP) pretreatments. Physicochemical changes were monitored by X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), and wet chemistry methods. Results show that free CaOX crystals affected negatively (by ca 39%) the saccharification of AHP-pretreated EAB compared to AGB. On the other hand, IL pretreatment achieved higher sugar yield (7.8 g dm(-3)) and lower crystallinity (14%) with EAB than for AHP (5.4 g dm(-3) and 29%, respectively). (C) 2016 Elsevier Ltd. All rights reserved.