One aspect of the invention relates to a process, comprising treating lignocellulosic biomass according to a first pretreatment protocol, thereby generating a first product mixture; separating the first product mixture into a first plurality of fractions; and treating at least one fraction of said first plurality of fractions according to a second pretreatment protocol, thereby generating a second product mixture. In one embodiment, the lignocellulosic biomass is selected from the group consisting of grass, switch grass, cord grass, rye grass, reed canary grass, miscanthus, sugar-processing residues, sugarcane bagasse, agricultural wastes, rice straw, rice hulls, barley straw, corn cobs, cereal straw, wheat straw, canola straw, oat straw, oat hulls, corn fiber, stover, soybean stover, corn stover, forestry wastes, recycled wood pulp protocol protocol fiber, paper sludge, sawdust, hardwood, softwood, and combinations thereof.