Silicon dioxide nanoparticles (SiO NPs) are commonly ingested by humans via food products, yet their potential biological effects remain poorly understood. To address this knowledge gap, we conducted a study to investigate the effects of a real food matrix and digestion on the behavior and toxicity of SiO NPs. The 25, 100, and 300 nm SiO particles (Si25, Si100, and Si300, respectively) were incubated with milk to simulate real-world conditions. Protein corona layers with varying thicknesses were observed for each particle. The main components of these corona layers were α- and β-caseins, and they were more abundant than whey proteins. Bare and milk-incubated particles went through a realistic digestion simulation with simulated saliva (SSF), gastric (SGF), and intestinal (SIF) fluids. TEM images revealed that the corona structure remained until the end of the digestion simulation. Toxicity analyses showed that as SiO NPs decreased in size, they exhibited more toxic effects on Caco-2 cells, regardless of digestion simulation. The corona mitigated the cytotoxicity of Si25. Additionally, we observed that SiO NPs induced reactive oxygen species (ROS) production depending on the particle size and corona formation. These findings have implications for the safe use of SiO NPs in consumer products and highlight the need for further research into the mechanisms underlying NP-induced ROS production and cytotoxicity.