Wheat is one of the world’s key staple foods, but it is often contaminated with mycotoxin-producing microorganisms, resulting in a large amount of food waste every year. The contamination of wheat grains harvested in 2020 and 2021 in Switzerland, as well as of wheat flours bought in local stores with the two mycotoxins zearalenone (ZEA) and enniatin B (ENB) was investigated. The quantification was performed using LC–MS/MS. ZEA, the level in different cereals and food products of which is regulated by law, was detected in half of the grain samples at levels below 100 µg/kg, except for one sample contaminated with 147 µg/kg. No ZEA was detected in the commercial wheat flours. The emerging mycotoxin ENB was detected in all samples of wheat grains and flours, at levels between 3 and 938 µg/kg. The harvest year was shown to affect the ENB content (p value < 0.01), and in particular the humid weather conditions encountered in 2021 during the month of harvest. The refining grade of the flours showed no influence on the contamination by ENB, indicating that the contamination with ENB can occur not only on the surface layers but also on the inner layers on the wheat grain. As chronic exposure to ENB can therefore not be excluded, decontamination solutions are needed to prevent food waste and further improve the food safety of wheat-based products.