The Atlantic king scallop, Pecten maximus, as a subtidal species is more and more exposed to fluctuations in water temperature and pH variations due to the ongoing climate change. Its ability to swim makes scallops exceptional between bivalves and previous studies have shown that ocean warming (OW) and acidification (OA) can impact swimming performance of P. maximus. In particular, warming induced a decrease in the muscular index as well as a reduction in force and strength of the adductor muscle of P. maximus. However, the metabolic mechanisms behind these observed limitations in muscle performance are largely unexplored. In this paper we present a semi-targeted metabolomic approach based on NMR spectroscopy for a retrospective study on frozen tissues of gill, mantle and adductor muscle of P. maximus, that were long-term acclimated under Ocean acidification, Ocean warming and the combination of both (OWA). 33 metabolites could be identified in all tissues, with organ depend differences in metabolite concentrations attributed to the specific functions of the individual organs. Metabolite changes to the different treatments showed that warming is the main driver for metabolic changes in gill and adductor muscle. In particular, energy-related metabolites, such as ATP and L-arginine, play an important role in the physiological response of scallops to OW and OWA. With the help of a combined approach of pathway analysis and network exploration the warming induced changes in energy-related metabolites could be attributed to the observed limitations in swimming performance of P. maximus.