In biorefinery procedures, pretreatment and conditioning of lignocellulose substrates are considered critical to enhance yields and rates of transformation. These processes use large volumes of water and chemicals, impacting the sustainability and economics of the biorefinery industry. In this study, we evaluate four pretreatment and conditioning process scenarios for removing acidic impurities from corn stover hydrolysate liquor, i.e., overliming, ammonia addition, two-stage treatment and membrane separations. The environmental impacts of these processes were determined using a life cycle assessment (LCA). Moreover, both the water and carbon footprints were estimated by considering energy and materials consumption. The results indicate that ammonia addition, two-stage treatment and membrane separations reduce environmental impacts in comparison to overliming. Integrated membrane separations exhibited the lowest water consumption (i.e., 2.5 L/kg-biomass) and carbon footprint (i.e., 6.2 g CO2/kg-biomass). In membrane separations, acidic impurities can be selectively recovered by electro-deionization as value-added products or reuse as process chemicals. Based on the LCA results, an integrated solution for hydrolysate pretreatment and conditioning is proposed as a cleaner and more sustainable process for the biorefinery industry. (C) 2016 Elsevier Ltd. All rights reserved.