"Masked mycotoxins" senso strictu are conjugates of mycotoxins resulting from metabolic pathways activated by the interplay between pathogenic fungi and infected plants. Zearalenone, an estrogenic mycotoxin produced by Fusarium spp, was the first masked mycotoxin ever described in the literature, but its biotransformation has been studied to a lesser extent if compared to other compounds such as deoxynivalenol. We presented herein the first application of organ and tissue culture techniques to study the metabolic fate of zearalenone in durum wheat, using an untargeted HR-LCMS approach. A complete, quick absorption of zearalenone by uninfected plant organs was noticed, and its biotransformation into a large spectrum of phase I and phase II metabolites has been depicted. Therefore, wheat organ tissue cultures can be effectively used as a biocatalytic tool for the production of masked mycotoxins, as well as a replicable model for the investigation of the interplay between mycotoxins and wheat physiology.