Bacillus cereus anaerobic growth on different carbohydrates (glucose, fructose, sucrose or glucose–fructose mixture) was examined in synthetic mMOD medium under continuous cultures (μ = 0·2 h−1). Fermentation end-products, flux partitioning at each key branch points of the mixed acid pathway and consumption or production of amino acids were determined. On both fructose and sucrose, ATP production was favoured via acetate production from acetyl-CoA. In addition, amino acids present in the growth medium showed significant variations with high consumption of serine and net production of glutamate and alanine on some or all sugars. Enterotoxins Hbl and Nhe production was high during growth on fructose (or mixtures involving a fructose moiety). Conclusions: Fructose was identified as a key sugar influencing anaerobic metabolism and toxin production of B. cereus. Significance and Impact of the Study: The physiological differences associated with the fermentation of the various carbohydrates clearly modify toxinogenesis indicating that the risk of foodborne pathogens is to some extent dependent upon the prevailing nutritional environment.