The industrialization of societies has gradually brought new problems to mankind. Among these challenges, producing significant amounts of industrial waste can be mentioned. These wastes are very diverse, and some are classified as hazardous (toxic) ones that, if not managed properly, will cause irreparable damage to the environment and, finally, to ourselves. On the other hand, industrial wastes are valuable materials for sustainable biomass production because they can be used as unlimited resources for energy generation or other value-added products; consequently, many authorities are looking for technologies to recycle and valorize waste. Recently, along with many chemical and mechanical methods developed, the use of microalgae and microorganisms has drawn much attention owing to their countless benefits, such as the degradation of hazardous organic wastes without producing more pollution. In the meantime, recent studies showed that the emergence of metabolic engineering may be able to improve efficiency rates by applying genetic engineering tools like overexpression, gene knockout, and synthetic biology techniques to re-design the pathways or introduce heterologous pathways to the desired organisms. Easy access to big data (omics) and simultaneous advances in computational methods, systems biology, and artificial intelligence (AI) have made it possible to manipulate organisms toward human goals easily. In this chapter, we first describe how microorganisms generate value-added products from various industrial wastes. Then, in-silico and in-vivo approaches in metabolic engineering are comprehensively defined, and at the end, some examples of recent developments in this field are reviewed.