One of the industrial sectors with the highest production in the world is agriculture, and therefore it is also one of the sectors that generate the greatest amount of waste. This waste is not used in its entirety and the remnants are disposed of in the correct way generating serious environmental problems. Agro-industrial waste includes a wide range of products of heterogeneous nature, which include seeds, husks, roots, stems, among others. These residues are characterized by a high content of proteins, carbohydrates or minerals so they could be used for the design of new human and animal foods, however, the content of toxic compounds limits their use. These 288residues are mostly characterized by having a high content of saponins, phytates, oxalates, alkaloids, among others, which have a negative effect on health. Therefore, it is necessary to apply treatments to be able to use these products. Biotechnological processes are a viable alternative to take advantage of these residues, given that during these toxic compounds are hydrolyzed and compounds are generated with biological activities such as antioxidants, antimicrobials, anticancer, antihypertensive, among others, which could have application in other industries such as pharmaceuticals. Nowadays, research to obtain biocompounds with these characteristics is growing since the beneficial effects of their consumption have been demonstrated. Therefore, fermentation processes are a profitable strategy to obtain high value-added biocompounds from agro-industrial residues. The objective of this chapter is to know the main toxic compounds present in agro-industrial waste and the biocompounds that can be generated from such waste according to the microorganism (bacteria, yeasts, fungi) used for fermentation.