To test the potential of diet switching experiments in ecophysiological studies of marine invertebrates, stable carbon isotope ratios were measured at different seasons in the gonad, adductor muscle, digestive gland and gills of scallops (Pecten maximus) and oysters (Crassostrea gigas) held for 15 days on a constant diet of phytoplankton depleted in 13C. The aim of this study was to determine if differences in carbon incorporation could be detected among species, seasons and organs, and if so, whether it was consistent with their known energy-allocation patterns. After offering the new diet, isotope values of the different organs gradually shifted and significant differences among organs, seasons and species were found. A carbon incorporation index (CII) was calculated to compare the metabolic activity of each organ of the two species between day 0 and day 15. For both species, the digestive gland had the highest CII, the adductor muscle the lowest, while gonad and gills had intermediate values. The CII was generally much higher in P. maximus than in C. gigas, suggesting higher metabolic activity in this species. Seasonal differences in the CII were also observed for the two species and were interpreted as differences in metabolic activity in accordance with our energy allocation scenario. Therefore, stable isotope diet switching experiments appear to be of great value for assessing metabolic orientation in bivalves.