This chapter focuses on the recent advances in the use of membrane processes for the recovery of biologically active compounds (BACs) from agro-food products and by-products. The fundamentals of typical membrane operations, as well as of membrane preparation, are firstly presented. Then, typical case studies for the recovery of polyphenols, peptides, carotenoids and tocopherols are presented and discussed. Multistep membrane processes for the separation, purification and concentration of BACs from their original sources are specifically designed based on laboratory experimental data. These processes provide concentrated fractions for the formulation of functional foods within a biorefinery strategy, with significant economic and environmental advantages over conventional methodologies.