Alcohols useful as fuel compositions are produced from biomass by pretreating the biomass prior to hydrolysis and fermentation. In the pretreatment, the biomass is contacted with an aqueous solution containing a dilute acid with concentration of up to 10 wt % producing a predigested stream containing an aqueous liquor that contains at least a portion of hemicelluloses and a residual biomass that contains celluloses and lignin; separating at least a portion of the aqueous liquor from the residual biomass providing an aqueous liquor stream and a pre-digested biomass stream; then contacting the pre-digested biomass stream with a cooking liquor containing at least one alkali selected from the group consisting of sodium hydroxide, sodium carbonate, sodium sulfide, potassium hydroxide, potassium carbonate, ammonium hydroxide, and mixtures thereof and water. A process that allows for higher recovery of carbohydrates and thereby increased yields is provided.