Many enzymes play significant roles in the biofuel industry for biomass pretreatment, enhancing oil recovery, reducing viscosity in fermentation broths, and breaking down complex substrates into simple sugars. After fermentation, enzymes produced for biofuel processing must be concentrated and stabilized as efficiently as possible. However, due to the low-cost requirements for biofuels, it is essential that these enzymes also have competitive production costs, even at the expense of purity levels. This chapter explores the critical steps in recovering, purifying, and formulating enzymes for biofuel production. It covers methods for extracting enzymes from fermentation broths, purifying them for high activity and stability, and formulating them for industrial applications. Stability, target activity concentration, and liquid formulations are given special focus. Furthermore, the chapter discusses in situ enzyme production with simplified downstream processing, highlighting how this approach can enhance process efficiency and cost-effectiveness.