The aim of this tutorial review is to provide a general overview of processes, technologies and challenges in the production of pharmaceutical and bioactive compounds from food waste and lignocellulosic residues. Particular attention is given to benign-by-design processes instinctively devoted to environmental sustainability for the recovery of bioactive compounds from food waste as well as for the production of alcohols, acids, polyols, furans and aromatic compounds from lignocellulosic residues. At the same time, novel green synthetic routes for the production of active pharmaceutical ingredients and the development of novel bioactive compounds are discussed. Recent success industrial stories on the use of food waste and lignocellulosic residues for pharmaceutical and nutraceutical applications are also discussed.