Lignocellulosic biomass can readily be converted to liquid fuels and be used as a replacement for fuels made from petroleum. One likely near-term transportation fuel is ethanol made by fermenting sugars derived from biomass.  One potential route for converting biomass to ethanol involves a series of thermochemical and biological steps to break down the biomass carbohydrate polymers to sugar and to subsequently ferment the sugars to ethanol. A thermochemical step or “pretreatment” modifies the biomass structure to improve enzymatic conversion of cellulose to glucose. After enzymatic conversion, the monomeric sugars are fermented to ethanol using a microorganism.  Because the process is complex, understanding how each step affects the other is necessary in process development.  In this study, we assessed performance of an integrated corn stover to ethanol process based on dilute sulfuric-acid pretreatment, ammonium hydroxide conditioning of the hemicellulosic liquor stream, enzymatic cellulose hydrolysis of the whole slurry (recombined hemicellulose stream and cellulosic solids), followed by co-fermentation of glucose and xylose. Conversion yields were measured for two different strains of Zymomonas mobilis, two different enzyme preparations and at a 17.5% and 20.0% (w/w) total solids loading. Key performance variables measured include cellulose conversion during enzymatic hydrolysis, conversion of sugars to ethanol and overall ethanol yield. The data was used to perform an economic analysis to understand the relevant impact on ethanol production cost. Using a combination of better enzymes and microorganisms we achieved an overall ethanol yield of 74.2 gal/dry ton, an 11% improvement over our initial starting value.