Pectinid species (scallops) hold significant economic value, but their filtration activity makes them vulnerable to harmful algal blooms, particularly Pseudo-nitzschia species producing domoic acid (DA). Domoic acid contamination can lead to amnesic shellfish poisoning in humans, causing prolonged fisheries closures and sales bans. This study aimed to compare several pectinid species to investigate if inter-specific differences in energetic traits could be linked to their ability to depurate the toxin. Using Dynamic Energy Budget (DEB) theory and the AmP multi-species estimation procedure, we analysed five species: two slow depurators (Pecten maximus and Placopecten magellanicus) and three hypothesised fast depurators (Argopecten purpuratus, Mimachlamys varia, and Nodipecten subnodosus). Results showed differences among species in assimilation rates, somatic maintenance rates, and reserve mobilisation rates but only the reserve mobilisation rates (i.e. the energy conductance parameter) consistently increased along the “slow-to-fast” depuration gradient. This research lays the groundwork for developing toxin kinetics models to quantify the processes affecting DA accumulation and depuration, and to assess the retention time of DA. Our approach and results will therefore not only be of interest to the DEB community in terms of multi-species approaches, but are likely to have applications in pectinid aquaculture and fisheries management.