BACKGROUNDThis study aims to obtain systematic understanding of the way by which pesticides are metabolized in plants and the influence of this process on plants' metabolism as this process has a key impact on plant‐based food safety and quality. The research was conducted under field conditions, which enabled to capture metabolic processes taking place in plants grown under multihectare cultivation conditions.RESULTSResearch was conducted on three wheat varieties cultivated under field conditions and treated by commercially available preparations (fungicides, herbicides, insecticides, and growth regulator). Plant tissues with distinctions in roots, green parts, and ears were collected periodically during spring–summer vegetation period, harvested grains were also investigated. Sample extracts were examined by chromatographic techniques coupled with tandem mass spectrometry for: dissipation kinetics study, identification of pesticide metabolites, and fingerprint‐based assessment of metabolic changes.CONCLUSIONTissue type and wheat varieties influenced pesticide dissipation kinetics and resulting metabolites. Metabolic changes of plants were influenced by type of applied pesticide and its concentration in plants tissues. Despite differences in plant metabolic response to pesticide stress during cultivation, grain metabolomes of all investigated wheat varieties were statistically similar. 4‐[cyclopropyl(hydroxy)methylidene]‐3,5‐dioxocyclo‐hexanecarboxylic acid and trans‐chrysantemic acid – metabolites of crop‐applied trinexapac‐ethyl and lambda‐cyhalothrin, respectively, were identified in cereal grains. These compounds were not considered to be present in cereal grains up to now. The research was conducted under field conditions, enabling the measurement of metabolic processes taking place in plants grown under large‐scale management conditions. © 2024 Society of Chemical Industry.