Lignocellulosic biomass pretreated by dilute acid produces monomeric hemicellulosic sugars and enhances the ability of enzymes to hydrolyze cellulose to glucose. However a conditioning process is usually required to remove compounds inhibitory to fermentative microorganisms. Previous work determined that an ammonium hydroxide conditioning (AHC) process decreased fermentable sugar losses and increased ethanol yields compared to a standard overliming process. The goal of this work was to 1) to rigorously quantify fermentable sugar losses (glucose and xylose) that occur during the AHC process, 2) determine the effect of conditioning pH on fermentation performance, and  3) investigate the effects of AHC liquor on enzymatic hydrolysis of dilute acid pretreated corn stover. The results indicate that regardless of the conditioning pH, the combined glucose and xylose loss was less than 1%, well below the 12% and 13% loss of glucose and xylose, respectively, previously determined using an overliming process. Fermentation testing showed that liquors treated at a conditioning pH of 6.8 and 8.0 achieved nearly identical ethanol yields of 70.3% and 71.6%, respectively. The best ethanol yield value of 79% was achieved with liquor conditioned at pH 8.5. At a conditioning pH of 9.0, the ethanol yield was dramatically reduced to 63%. Although ammonia conditioning led to improved fermentation performance, it had a slight inhibitory effect on enzymatic hydrolysis. Enzymatic cellulose conversion of pretreated corn stover solids in the presence of AHC liquor was reduced by 2% to 6% depending on enzyme dosage compared to solids in the presence of overlimed liquor.