Bioactive compounds are a group of compounds that may or may not occur naturally and can have an effect on human health. Polyphenols and polypeptides are examples of such compounds. In order to improve functional properties of foods, several processes have been used to obtain and purify these compounds having high added values. The extraction processes of these compounds include chemical synthesis, particularly used in food industry, distillation, solvent and supercritical fluids extraction. On the other hand, soft chemistry provides new routes for a set of mild chemical operations, which can contemplate reactions such as cationic exchange, dehydration, hydrolysis, redox, among others. These reactions could be found in biological processes. Microorganisms have the ability to synthesize these molecules and the efficiency of enzymes in the degradation and synthesis of compounds. Fermentation and enzyme-assisted extraction form the part of new methodologies to obtain bioactive compounds.