Stored wheat grains are colonized by a wide range of saprophytic and pathogenic fungi. Contamination by mycotoxigenic species like Fusarium spp. raise concern about the food safety of the commodity. Different environmental and genetic factors govern colonization. The present work studies the relationships between the wheat variety and the resistance against Fusarium head blight (FHB) among the diversity of grain colonizers. Five Swiss and five Polish varieties were planted in an experimental site, and the grains were harvested and stored according to a unified protocol in order to avoid contamination during and after harvest. In parallel, the resistance of the varieties was established by conducting trials at two other experimental sites with artificial infections. Overall, about 18 fungal taxa were identified on the grains from the plot trial. Results show significant differences in the presence and abundance of fungal species between the varieties. Colonization, in particular with Fusarium spp., was not correlated with FHB resistance. The experiments demonstrate that the factor variety can influence the colonization of wheat grains by fungi. Future research must help to better understand the plant traits that govern the differential colonization. These findings should be considered in future studies on wheat storage and food safety.