Environmentally persistent free radicals (EPFRs) may pose a potential risk to the ecosystem and human health via oxidation stress and are considered emerging contaminants. Being stable with a lifetime of minutes or several months and abundant in transitional matrices (e.g. biochar), EPFRs continue to affect deposits (e.g. soil) and related media (plants) when the transitional matrices (e.g. biochar) are applied. The impact of EPFR on the plant uptake of chemical elements (CEs) was studied in the field conditions where, for two years, biochar and fertilisers were applied to the agricultural soil for winter triticale cultivation. EPFRs determination methods, along with the element uptake indices (bioaccumulation and biophilicity) and the method of the dynamic factors were applied. Results have shown that EPFRs have influenced the soil properties relevant to CE soil bioavailability and bioaccumulation in plants. The impact of EPFRs on CE transport in the soil–plant system was observed to influence the biogeochemical behaviour of CEs in the soil–plant system. This work provides the first findings on EPFRs-induces changes on CE bioavailability and bioaccumulation intensity, indicating the higher plant uptake risk of some potentially toxic elements (such as Cr).