Corn-based breakfast cereals, known as cornflakes, have become a common breakfast choice worldwide, recognized for their convenience and versatility. However, mycotoxins can contaminate these products, adversely affecting human health. This study assessed the occurrence of major mycotoxins (AFB1, OTA, DON, ZEA, and FUM) in cornflake stock-keeping units (SKUs) marketed in the United Arab Emirates (UAE). It also evaluated the effect of different independent variables (country of origin, temperature on the production day, storage time, presence of chocolate, bran, and nut ingredients) and estimated the exposure levels of the UAE population to these mycotoxins and the associated risk factors. Seventy-six distinct cornflake SKUs were identified through a market screening and tested for mycotoxins using the Enzyme-Linked Immunosorbent Assay (ELISA) technique. AFB1, OTA, ZEA, FUM, and DON were detected in 23.7, 48.7, 27.6, 9.2 and 88.2% of the samples, respectively. The mean concentrations among positive samples were 2.0, 1.0, 10.14, 584.9, and 90.6 μg/kg, respectively. Except for AFB1, the average mycotoxin levels in samples were below the established limits by the European Union (EU). Among positive samples, none exceeded the US FDA limits for all mycotoxins, and only one exceeded the CODEX limit for FUM. On the other hand, four (5.3%), one (1.3%), one (1.3%), and one (1.3%) SKU exceeded EU limits for AFB1, OTA, FUM, and ZEA, respectively. The country of origin (developing vs. developed countries) exhibited a significant effect on AFB1 presence (p < 0.0001). Furthermore, higher temperature on the production day was associated with significantly higher AFB1 occurrence (p = 0.009). Moreover, the presence of chocolate ingredient had a borderline significant effect on AFB1 (p = 0.05) and a significant effect on OTA (p = 0.002), with higher percentages observed in SKUs containing chocolate. However, no significant effects were found for storage time or the presence of bran and nut ingredients in the cornflakes. On the other hand, the HQ values were below 1 for all mycotoxins, indicating low risk. MoE values exceeded 10,000 among regular cornflake consumers, except for FUM, suggesting minimal risk. Liver cancer risk was 0.0032 cases per 100,000 people per year. Weekly OTA exposure was 0.133 ng/kg BW, below PTWI (Provisional Tolerable Weekly Intake).