Biofuels can be produced by: (i) providing a biomass containing celluloses, hemicelluloses, lignin, nitrogen compounds and sulfur compounds; (ii) removing sulfur compounds and nitrogen compounds from the biomass by contacting the biomass with a digestive solvent to form a pretreated biomass containing carbohydrates and having less than 35% of the sulfur content and less than 35% of the nitrogen content of untreated biomass on a dry mass basis; (iii) contacting the pretreated biomass directly with hydrogen in the presence of a hydrogenolysis catalyst to form a plurality of oxygenated intermediates, and (vi) processing at least a portion of the oxygenated intermediates to form a liquid fuel.