The occurrence of deoxynivalenol, nivalenol and deoxynivalenol-3-glucoside in 104 corn and wheat flour samples available on the Egyptian market was investigated using ultra-performance liquid chromatography with a photodiode array detector (UPLC-PDA). Of all samples, 70.2% were contaminated with deoxynivalenol at levels varying between < LOQ and 853 μg/kg. Nivalenol and deoxynivalenol-3-glucoside were detected in only 54.8% (range < LOQ–462 μg/kg) and 32.7% (range < LOQ–257 μg/kg) of the samples, respectively. The occurrence of the target mycotoxins was more frequent in corn flour samples, compared to wheat flour ones (p < 0.05). A total of 46.6% (34/73) of all deoxynivalenol-positive samples contained glucoside conjugate form (deoxynivalenol-3-glucoside) at contamination levels that reached 8.0–33.3% of the parent deoxynivalenol. To the best of our knowledge, this is the first report of deoxynivalenol-3-glucoside in cereal-derived products from Egypt. Dietary risk assessment was also conducted by evaluating the probable daily intakes, which were within the tolerable daily intakes proposed by the Scientific Committee for Food (SCF) of the European Union for legislated mycotoxins (0.7 and 1.0 μg/kg body weight/day for NIV and DON, respectively). However, from the food safety's point of view, the co-occurrence of mycotoxins across a high number of the analyzed samples (64/104) would increase the toxicological hazard due to synergistic effects of possible combined exposure. Still, the need for continuous surveillance of these mycotoxins throughout the cereal production chain is important to control and minimize their potential health hazards, particularly those attributed to DON intake by the consumers.