Nutritional composition and neo-formed contaminant content in ultra-processed foods, amongst other factors, may contribute to increasing overall risk of non-communicable diseases and cancer. Commercial breakfast cereals (n = 53) were classified according to the NOVA approach as un-/minimally processed (NOVA-1, 11%), processed (NOVA-3, 30%), and ultra-processed (NOVA-4, 59%) foods. Acrylamide and hydroxymethylfurfural (HMF) content as heat-induced chemical markers was taken from our research team database. The NutriScore was used as the nutritional profiling system. Samples were distributed between groups A (19%), B (13%), C (38%), and D (30%). No statistically significant differences in acrylamide and HMF were found across the NutriScore groups. Sugar content was the only nutritional descriptor found to be significantly different between processed (11.6 g/100 g) and ultra-processed (23.1 g/100 g) breakfast cereal groups. Sugar content correlated with acrylamide (p < 0.001) and HMF (p < 0.0001). Acrylamide and HMF contents were not significantly higher in the NOVA-4 group when compared with the NOVA-3 group. However, trends towards higher acrylamide and HMF content are observed, amounting to a change of 75 µg/kg and 13.3 mg/kg in processed breakfast cereals, and 142 µg/kg and 32.1 mg/kg in ultra-processed breakfast cereals, respectively. Thus, the NOVA classification may not reflect the extent of the thermal treatment applied to the breakfast cereal but the type and amount of ingredients incorporated. Ultra-processed breakfast cereal does not predict significantly higher toxicological concern based on acrylamide content than processed breakfast cereals; a clear trend is seen whose contributing factors should be further studied.