Single conidia strains of Fusarium poae and Fusarium avenaceum were investigated for their ability to synthesise mycotoxins in vitro. In a first experiment, rice was inoculated with three strains of F. poae and three strains of F. avenaceum. In a second experiment, the same strains were cultivated on four different cereal substrates. For both experiments, the colonised substrates were analysed using liquid chromatography coupled with tandem mass spectrometric detection (LC-MS/MS) for the content of Fusarium mycotoxins. On rice, a strong effect of strains on mycotoxin content was found. With the analyses of different cereal types, substantial substrate effects were observed. For F. poae, these effects were highly dependent on the strain. The results of this study are of benefit for risk assessment concerning naturally infected grain samples since substrate effects could also be triggered by different cereal species or varieties, and thus could lead to variable mycotoxin contamination in cereal products intended for human consumption.