A process is provided for the recovery of holocellulose sugars and a near-native lignin co-product from lignocellulosic biomass. The cellulose produced from the process is amenable to subsequent enzymatic hydrolysis to produce monomeric sugar units which can be combined with hemicelluloses-derived sugar units to be co-fermented to produce biofuels and/or chemicals. The process can include either single or multiple hydrothermal treatments of the biomass in aqueous solution under pressure at selected pH and temperature conditions to produce a first liquid phase containing mostly hemicellulose sugars, and a first solid stage containing native lignin. The first solid phase can be subjected to an organosolv treatment to produce a second liquid phase containing most of the near-native lignin as a dissolved component, and a second solid phase containing mostly cellulose. The second liquid phase can be processed to recover near-native lignin powder. The second solid phase can be exposed to hydrolysis enzymes and fermentation yeasts and/or recombinant organisms to produce a biofuel or biochemical. The second solid phase can further be combined with the first liquid phase so as to allow simultaneous saccharification and co-fermentation of the holocellulose-derived sugars.