Titanium dioxide nanoparticles (TiO2 NPs) are widely used in industry as a white pigment (paints, paper industry and toothpastes), photocatalysts (environmental decontamination and photovoltaic cells), inorganic UV filter (sunscreens and personal care products) and as a food additive (E171) and antimicrobial food packaging material. Silver nanoparticles (Ag NPs) are used in photonics, microelectronics, catalysis and medicine due to their catalytic activity, magnetic and optical polarizability, electrical and thermal conductivities and enhanced Raman scattering. They also have antibacterial, antifungal and antiviral activities, as well as anti-inflammatory potential. The huge increase in the use of nano-based products, mainly metallic NPs, implies the presence of nanomaterials in the environment, and hence, the unintentional human ingestion through water or foods (gastrointestinal tract is the main pathway of NPs intake in humans). The presence of TiO2 NPs and Ag NPs in seafood samples was firstly established using an ultrasound assisted enzymatic hydrolysis procedure and sp-ICP-MS analysis. Several clams, cockles, mussels, razor clams, oysters and variegated scallops, which contain TiO2 NPs and Ag NPs, were subjected to an in vitro digestion process simulating human gastrointestinal digestion in the stomach and in the small and large intestine to determine the bioaccessibility of these NPs. Caco-2 cells were selected as model of human intestinal epithelium for transport studies because of the development of membrane transporters that are responsible for the uptake of chemicals. Parameters as transepithelial electrical resistance (TEER) and permeability of Lucifer Yellow were studied for establishing cell monolayer integrity. TiO2 NPs and Ag NPs transport as well as total Ti and Ag concentrations passing through the gastrointestinal epithelial barrier model (0–2 h) were assessed by sp-ICP-MS and ICP-MS in several molluscs. Display omitted •Moderate bioaccessibility ratios of TiO2 and Ag nanoparticles in commercial fresh and frozen bivalve molluscs.•TiO2 and Ag nanoparticles transport assay by Caco-2 cells successfully applied to bivalve molluscs.•High sensitivity of single particle ICP-MS for characterizing TiO2 and Ag nanoparticles.