Mycotoxin contamination in agricultural products is a significant food safety and public health concern globally. However, little is known about the occurrence and levels of deoxynivalenol (DON) and zearalenone (ZEN) in agri-food product in Chile. In this study, high-performance liquid chromatography coupled with fluorescence detection (HPLC-FLD) and ultraviolet detector (HPLC-UV) were employed to analyze the levels of ZEN and DON in oats, wheat flour, and cereals marketed in Chile and assess the exposure of Chilean individuals through the consumption. The presence of ZEN and DON during 2016–2022 was not considerable. Nonetheless, a higher prevalence of DON was observed in wheat flour (6.1 %) than in cereals (1.2 %) in different regions of Chile, without concentrations exceeding national regulations (750 ngg−1). The only positive sample for ZEN exceeded the international regulations (75 ngg−1) for cereals by 30-fold (2302 ngg−1). The Estimated daily intake (EDI) and Hazard quotient (HQ) for DON indicated no risk to human health. Meanwhile, the EDI for ZEN exceeded the Tolerable daily intake (TDI: 250 ngkg−1 day). Consequently, the HQ for ZEN was 7.7 (2–5 years) and 4.3 (6–13years), indicating a risk to children and adolescents, which are vulnerable age groups. We recommended increasing the frequency of mycotoxin monitoring for highly consumed agri-food products, considering that Chile is highly susceptible to the effects of climate change that promote the natural proliferation of mycotoxins.