We have investigated a modification of the SAA method, a Soaking in Ethanol and Aqueous Ammonia method (SEAA), to reduce the loss of xylan due to solubilization. In this method ethanol is added to the aqueous ammonia solution. The presence of ethanol causes re-precipitation of the previously solubilized xylan onto the solid matrix. Thus more xylan is available for conversion to ethanol. The ethanol used in the pretreatment process can be recovered and recycled. In addition to increased availability of the carbohydrates for ethanol production, the solubilized lignin theoretically can be recovered in relatively pure form and converted to high-value products. Re-precipitation of the solubilized xylan does not affect the bioconversion efficiency of the pretreated biomass. The pretreated biomass can be converted to ethanol or chemicals in the simultaneous saccharification and co-fermentation (SSCF).