This study aims to provide information on the behaviour and biopersistence rate (BP) of metallic nanoparticles (Ag-NPs, TiO2-NPs, ZnO-NPs) naturally occurring in canned seafood and subjected to static in vitro digestion. Single particle ICP-MS analysis was performed to determine NPs distribution and concentrations in oral, gastric, and intestinal digests. Depending on the conditions of the digestive phase and the sample matrix, the phenomena of agglomeration and dispersion were highlighted and confirmed by Dynamic Light Scattering (DLS) technique. In standard suspensions, Ag-NPs had lower biopersistence (BP) than ZnO and TiO2-NPs (BP 34%, 89% and >100%, respectively). Among Ag-NPs and TiO2-NPs naturally present in the food matrix, those in canned tuna were more degradable than those in canned clam (BP Ag-NPs 36% vs. > 100%; BP TiO2-NPs 96% vs. > 100%), while BP ZnO-NPs showed high biopersistence in both seafood matrix (>100%). The biopersistence rates were higher than the recommended limit set by European Food Safety Authority (EFSA) (12%), referred to nanotechnologies to be applied in the food and feed chain, thus the investigated naturally occurring NPs cannot be considered readily degradable.