The investigation of novel biotechnologyBiotechnology techniques has been sparked by the increasing need for sustainable methods in the use and processing of agro-industrial wastes. A key component of biotechnology, microbialMicrobial transformationsMicrobial transformation provide economical, ecologically benign and effective methods for turning wastes rich in organic matter into products with added value. These wastes have important commercial and medicinal uses as possible feedstocks for synthesising pigments, enzymes, bioactive chemicals, biofuelsBiofuels, as well as biopolymersBiopolymers. Novel extraction methods, namely supercritical fluid, ultrasound-assisted, as well as pulsed electric field extraction, as well as strain engineering, enzyme immobilisation, morphological engineering and genome editing, have shown promise in improving the qualitative and quantitative characteristics of bioproducts. The global emphasis on biowaste valorisationBiowaste valorisation has accelerated the commercialisation of these products, reshaping markets and creating new investment opportunities. Even so, it is still challenging to develop products and recover them from raw materials using upstream microbialMicrobial processing, but these problems can be addressed by optimising bioreactor designs, modifying conditions and using alternative techniques. More effort should also be made to ensure that goods are stable, affordable and scalable. This chapter explores the most recent developments, new possibilities, and existing problems in using agro-industrial waste, with a special emphasis on how this can help the bioeconomyBioeconomy.