Screening experiments were conducted using an automated microwave reactor pretreating two algal strains, Scenedesmus and Chlorella, at 7% solids loading (w/w). Reaction conditions leading to enhanced carbohydrate and lipid release were scaled 20% solids loading (w/w) pretreated using a steam injected Zipperclave reactor. After pretreatment the slurry was centrifuged with the liquor fraction fermented to ethanol with yields approaching 91% (w/w). The protein and lipid component were collected into the solid fraction and later extracted for characterization. The process was further scaled to pilot scale utilizing 130-kg pretreatment reactor at 25% solids loading (w/w). Ethanol yield of the algal hydrolyzate approached 79% (w/w) in less than 20 hours. Hexane extraction of the solid fraction yielded a lipid content in the solid fraction approaching 45% (w/w). Based on these results we present an integrated approach to bioprocessing of algal biomass examining the impact of scale, % solids loading and reactor type on the pretreatment and fractionation process.