Human bivalve consumption in Europe has steadily increased in the last years, particularly during summer months when seawater temperature increases. Since ocean warming is among the current global environmental threats affecting aquatic organisms, it is of paramount importance to investigate its effect on the nutritional quality of seafood products. In this context, the aim of this study was to investigate differences in the nutritional quality (in terms of protein, glycogen and fatty acid, FA, content) and condition of a native (grooved carpet shell, Ruditapes decussatus) and an invasive (Japanese carpet shell, Ruditapes philippinarum) clam species, subjected to warming. Our results clearly reveal that temperature significantly affected the nutritional quality of both clam species, particularly the FA composition. Both clam species responded similarly to warming, by significantly decreasing the content of some fatty acids, but not protein and glycogen levels. A predominance of polyunsaturated FA (PUFA) over saturated FA (SFA) and monounsaturated FA (MUFA) was observed throughout the experiment, as well as high n − 3/n − 6 and PUFA/SFA ratios. The native clam always revealed higher values of these fatty acids, indicating that this species has a better nutritional quality in comparison to the invasive one. Nonetheless, the loss of n − 3 PUFA (in native species), eicosapentaenoic (EPA; in both species) and docosahexaenoic (DHA; in invasive species) acids was considered as the major negative outcome derived from warming, since it contributes to the loss of prime quality fatty acids for human health. However, atherogenic, thrombogenic and hypocholesterolemic/hypercholesterolemic indices (AI, TI and h/H, respectively) remained low in both species, even in warming conditions, suggesting that these food items can be used in a cardio-protective and hypocholesterolemic diet. This study provides new insights to understand and foretell the effects of climate change on nutritional quality of marine organisms.