The present invention generally provides methods of improving lignin separation during biomass fractionation with an acid to release sugars and a solvent for lignin (such as ethanol). In some embodiments, a digestor is employed to fractionating a feedstock in the presence of a solvent for lignin, sulfur dioxide, and water, to produce a liquor containing hemicellulose, cellulose-rich solids, and lignin. A solid additive is added to the digestor, wherein the solid additive combines with at least a portion of the lignin. Then a mixture of lignin and the solid additive is separated from the liquor, prior to hemicellulose recovery. Optionally, a solid additive may also be introduced to a hydrolysis reactor for converting hemicellulose oligomers to monomers, to improve separation of acid-catalyzed lignin. In some embodiments, the solid additive is gypsum or a gypsum/lignin mixture.