The biorefinery systems of marine biomass to recover valuable biocompounds is an emerging field in the context of efficient and sustainable management of resources. Among the distinct strategies with high potential at an industrial scale for valorisation, fish protein hydrolysates (FPH) stand out. These can be obtained from previously discarded biomass, fish processing by-products and by-catches. Such FPH contain unique bioactive peptides with a wide range of biological activities of interest in multiple areas. Therefore, evaluating the environmental impact of these valorisation processes to ensure their sustainability before industrial scale implementation is crucial. Life cycle assessment (LCA) is an appropriate tool. However, one of the most critical issues is properly accounting for the impact of certain pollutants released into the environment, such as engineered nanoparticles (ENPs). It has been stated that increased products embedded with ENPs could pose risks to biodiversity, particularly in the marine environment. The main objective of this chapter is to provide a perspective on the application of LCA in the context of emerging technologies, highlighting current limitations and the need to develop strategies to quantify the impacts linked to the release of ENPs into the marine environment, ensuring safety across the value chain of FPH.