Currently, the EU is focusing on less intensive agrotechnology and sustainable development. It is important to minimize the occurrence of mycotoxins (including Fusariotixins) in food, and to monitor mycotoxin concentration in the food chain. Therefore, this study evaluated Fusarium mycotoxin contamination, specifically type A and B trichothecenes and ergosterol concentration, in wheat grain from a three-year field experiment (2019–2021) conducted at IUNG-PIB in Osiny (Poland), along with its byproducts (bran, flour, bread). Four wheat cultivars were grown under different farming systems: organic (ORG), integrated (INT), and conventional (CONV). Ergosterol was analyzed using HPLC with an absorbance detector while Type A and B trichothecenes were analyzed using gas chromatography and mass spectrometry. Results showed that the farming system significantly influenced type B trichothecenes concentration in grain, with the highest concentration established in ORG-grown wheat. However, the grain concentration from the INT farming system was comparable to that from CONV. Type A trichothecenes concentrations were low and not significantly affected by the farming system. Bran exhibited the highest ergosterol and mycotoxin concentration, while flour and bread exhibited the lowest.