The ammonia fiber expansion (AFEX) process has been shown to be an effective pretreatment for lignocellulosic biomass. Technological advances in AFEX have been made since previous cost estimates were developed for this process. Recent research has enabled lower overall ammonia requirements, reduced ammonia concentrations, and reduced enzyme loadings while still maintaining high conversions of glucan and xylan to monomeric sugars. A new ammonia recovery approach has also been developed. Capital and operating costs for the AFEX process, as part of an overall biorefining system producing fuel ethanol from biomass have been developed based on these new research results. These new cost estimates are presented and compared to previous estimates. Two biological processing options within the overall biorefinery are also compared, namely consolidated bioprocessing (CBP) and enzymatic hydrolysis followed by fermentation. Using updated parameters and ammonia recovery configurations, the cost of ethanol production utilizing AFEX is calculated. These calculations indicate that the minimum ethanol selling price (MESP) has been reduced from $1.41/gal to $0.81/gal.