Pesticides that are absorbed by plants undergo biotransformation and might affect plant metabolic processes. The metabolisms of two cultivated wheat varieties, Fidelius and Tobak, treated with commercially available fungicides (fluodioxonil, fluxapyroxad, and triticonazole) and herbicides (diflufenican, florasulam, and penoxsulam) were studied under field conditions. The results provide novel insights regarding the effects of these pesticides on plant metabolic processes. Plants (roots and shoots) were sampled six times during the six-week experiment. Pesticides and pesticide metabolites were identified using GC–MS/MS, LC–MS/MS, and LC–HRMS, while root and shoot metabolic fingerprints were determined using non-targeted analysis. Fungicide dissipation kinetics were analyzed according to the quadratic mechanism (R2: 0.8522–0.9164) for Fidelius roots, and zero-order for Tobak roots (R2: 0.8455–0.9194); shoot dissipation kinetics were analyzed according to first-order (R2: 0.9593–0.9807) and quadratic (R2: 0.8415–0.9487) mechanisms for Fidelius and Tobak, respectively. The fungicide degradation kinetics were different compared to reported literature values, most likely due to differences in pesticide application methods. The following metabolites were respectively identified in shoot extracts of both wheat varieties for fluxapyroxad, triticonazole, and penoxsulam: 3-(difluoromethyl)-N-(3',4',5'-trifluorobiphenyl-2-yl)-1H pyrazole-4-carboxamide, 2-chloro-5-{(E)-[2-hydroxy-3,3-dimethyl-2-(1H-1,2,4-triazol-1-ylmethyl)-cyclopentylidene]-methyl}phenol, and N-(5,8-dimethoxy[1,2,4]triazolo[1,5-c]pyrimidin-2-yl)-2,4-dihydroxy-6 (trifluoromethyl)benzene sulfonamide. Metabolite dissipation kinetics varied depending on the wheat variety. These compounds were more persistent than parent compounds. Despite having the same cultivation conditions, the two wheat varieties varied in their metabolic fingerprints. The study revealed that pesticide metabolism has a greater dependence on plant variety and method of administration compared to the physicochemical properties of the active substance. This highlights the necessity of conducting research on pesticide metabolism under field conditions.