Every year in France, seed producers must downgrade more than 12,000 tons of seeds. These seeds are currently incinerated in cement factories at seed producers’ expenses and non-available for the processes of valorization of renewable resources, due to their significant pesticide content. Consequently, the quantity of pesticides present in the seed loading must be reduced before a subsequent valorization of the downgraded seeds. The purpose of this work is thus to develop a process for the decomposition of a large amount of the pesticides present in the seed loading. Ozonation was proved to be efficient in wastewater treatment for the removal of pesticides of interest, usually present in the seed loading. Consequently, ozone was applied to soft wheat seeds loaded with Gaucho Ble´ loading solution, in a fixed bed reactor. The humidification of seeds before ozonation, the concentration of ozone in the inlet gas and the ozonation time were revealed to be the predominant factors to accelerate the kinetics of degradation of pesticides in the seed loadings. Using optimal conditions (determined by a Box–Behnken experimental design), pesticides were successfully decomposed (respectively 99 and 90% for the degradation of imidacloprid and bitertanol), within 96 min of treatment. The kinetic laws for the ozonation reactions of both pesticides were also determined and the partial orders of the reaction were 1 for both ozone and the pesticide. The subsequent application of this process for the treatment of other loaded seeds showed good degradation yields for all the studied pesticides and demonstrated the interest of such a process for the removal of pesticides on loaded seeds.