The seafood supply chain is adversely affected by significant losses and waste of resources, which include bycatch (the low value fish caught unintentionally during fishing), large amounts of process discards, and effluents released during seafood product development. These resources, collectively designated as seafood side streams, are usually discarded in the ocean or landfills, causing both loss of valuable compounds and serious environmental pollution. The purpose of this chapter is to present methods to make use of side streams as resources of useable products including proteins, lipids, minerals, chitin, and other compounds managed in an environmentally friendly manner employing green processing strategies. These involve initial microbial or enzymatic bioconversions to detach the compounds from seafood matrices, followed by their recovery by green solvents and other environmentally friendly procedures. Integration of the strategies on a biorefinery and circular economy protocol recovers optimally these compounds, while minimizing waste. The benefits of green processing of seafood side streams to improve blue economy of the seafood industry are discussed.