The aim of the present work was to investigate the interaction of nanoparticles (NPs) with proteins during the digestion of selected food matrices. To accomplish this, magnetic silica NPs were added to skimmed milk powder (SMP), peanuts, and tofu, and the mixtures were subjected to in vitro digestion. The proteins and peptides present in the digesta, with and without NPs, and in the protein corona (PC) of NPs at the different digestion stages (oral, gastric, and intestinal) were characterised and identified with gel electrophoresis and mass spectrometry. Electrophoretic results revealed no differences in protein patterns between the control and NPs containing digesta at all digestion stages. At the end of simulated intestinal digestion, no intact food proteins were detectable, either in the food or on the NPs. At this stage, exclusively, digestive enzymes originating from pancreatin were present in the digesta and bound to NPs. Digestion-resistant peptides were detected in the digests of all studied food matrices, independently of NP presence. Moreover, on the PC of NPs digestion-resistant peptides, especially longer ones, were exclusively present after gastric and intestinal digestion stages from SMP and peanuts, but not from tofu, indicating that the PC composition was influenced by the food matrix.