The effect of Fusarium spp. contamination on baking quality of winter common wheat and spelt wheat from different growing systems (organic and conventional) was evaluated by the standard technological quality characteristics and by the rheological system Mixolab. The content of Fusarium spp. mycotoxins [deoxynivalenol (DON), deoxynivalenol-3-β-d-glucoside (D3G), 3-acetyldeoxynivalenol (3-ADON), and Zearalenones (ZON)] was determined too. Significantly worse standard technological quality parameters and rheological parameters were determined for artificially inoculated variants of both evaluated wheat species. Statistically significant negative correlation coefficients were discovered between content of mycotoxins and many of technological characteristics, for example, DON content and Zeleny sedimentation for common wheat and spelt (−0.60*; −0.66*) and also between DON content and volume weight (−0.63*; −0.95**) for both wheat species. Resulted Mixolab parameters confirmed that Fusarium spp. infection worsens both protein and starch characteristics for both wheat species. However, effect of Fusarium spp. contamination in spelt wheat was generally less pronounced in comparison with common wheat. Despite of visible shifts of Mixolab curves of samples from organic and conventional growing systems, resulted Mixolab characteristics were statistically comparable.