The Gambian and Malian fisheries and fish processing value chains are predominantly artisanal and represent a key source of protein and livelihoods, yet their eco-efficiency has not been studied to date. A Life Cycle Assessment was used to estimate the associated environmental impacts of those value chains and provide information on the eco-efficiency indicators, which relate technical efficiencies to environmental impacts. The results showed that industrial Gambian fleets' fuel use efficiency is rather low as compared with the global mean fuel use intensity (landed fish/consumed fuel) for both small pelagics and demersal fish. In Mali, the fuel use intensity of motorised artisanal fisheries is lower than the mean values for artisanal inland fisheries in developing countries, but the important increase of frozen imported fish from fish farming multiplies the estimated impacts by four. The least energy-intensive fisheries (cast nets and stow nets in Gambia and opportunistic fishers in Mali) feature better eco-efficiency scores. Based on the identified sources of inefficiencies, we suggest improvements in the landing/processing infrastructure and fishing units' engines, coupled with technical and business training and improved processing methods, to ameliorate seafood eco-efficiency and a stronger recognition of the importance of the artisanal fisheries subsector to overcome challenges and improving resource management.