In Mediterranean countries, a large toxic effluents are produced by the agro-industrial activities that have to be disposed, being an environmental problem. On the other hand, due to the high organic load content they can be valorized in terms of energy production. Moreover, because most of them are rich in phenolic compounds (olive mill, cork boiling and chestnut wastewaters), a further valorization may be done to extract valuable biomolecules (bioactive compounds and enzyme) in a biorefinery approach. Aims of the presentation are: a) develop a innovative anaerobic digester, equipped with a monitoring and controlling systems, that will be used to valorize efficiently different phenolic agro-industrial effluents; b) recover valuable molecules with antioxidant and antiradical activity and enzymes, utilizing several novel and eco-friendly extraction systems; c) give solutions, to environmental problems and increase the efficiency and incomes of Mediterranean agro-industrial sector.