Dilute acid pretreatment of lignocellulosic biomass releases hemicellulosic sugars and improves the enzymatic digestibility of the treated solids, but the hydrolysate is often toxic to microorganisms. Several processes have been proposed to reduce hydrolysate toxicity including treating the liquor with lime or ammonium hydroxide. We investigated the impact of both of these chemicals on the performance of two different process configurations for producing ethanol from corn stover. In one process configuration, the hydrolysate liquor was removed from pretreated slurry and treated with lime or ammonium hydroxide. The liquor was recombined with the solids, the solids were enzymatically hydrolyzed to glucose with cellulase and the resulting sugar solution was fermented to ethanol using a glucose-xylose fermenting Z. mobilis. In the second process configuration, the whole slurry was treated with lime or ammonium hydroxide, and then the procedure used for the first process configuration was followed. Both process configurations were tested at a 15% and 20% (w/w) total solids loading at the enzymatic hydrolysis step. Neither lime nor ammonium hydroxide had a large impact on performance regardless of the process configuration or solids loading. For the first process configuration at a 20% total solids loading, cellulose to glucose yields of 74.3% and 75.6% and ethanol yields of 79.3% and 79.6% were achieved using lime or ammonium hydroxide, respectively. However, compared to lime, ammonium hydroxide eliminates sugar losses seen during the overliming process, the need to dispose of gypsum, and the potential for deposition of gypsum in downstream process equipment.