Traditionally, different techniques have been used for the recovery of bioactive compounds from waste and by-products of the agri-food industry, such as milling, extraction with solvents, etc. Innovative extraction technologies are, in general, more “green” technologies than conventional ones for the extraction of bioactive compounds. Vegetable and fruit processing industries produce millions of tons of by-products such as peels, seeds, stones, residual pulp, and discarded pieces that generate important environmental management problems for the industry. The waste obtained from fruits and processing industry is extremely diverse due to the use of a wide variety of fruits and vegetables, the broad range of processes, and the multiplicity of the product. Marine industry includes fish, macro- and microalgae, among other products. Based on the evidence of potential health benefits, bioactive peptides derived from fish by-products have promising applications as natural nutraceuticals. Scientific information about the applications of waste and by-products from the food industry are very extensive.