Multidimensional chromatographies (MDC) implying either a single column with an unique packing designed for providing several separation modes such as internal surface reversed-phase (ISRP), or C1 large pores particles, or multi-column switching technique using the previous supports as guard columns, allow fast and easy direct monitoring of pesticides into plant or animal biological media. In such a way, the comparative study of the agricultural fungicide cymoxanil in two strains of Botrytis cinerea of different sensitivities gave concordant conclusions with the previous work using radiolabelled cymoxanil and TLC. Moreover, as a comparison, a study of the metabolism of this xenobiotic was also followed in animal biological fluids likely to contain peptidases. In locust or lobster haemolymph, an unusual isomerization into a cyclic compound was thus demonstrated accompanying the classical peptidase-depending metabolism generally observed in plants. The same chromatographic approaches were tested and compared for monitoring the metabolism of the natural insecticide toxin E-destruxin in insects. A detoxication process leading to the less toxic E-diol destruxin was evidenced in the organs or haemolymph of the locust Locusta migratoria chosen as a model of non-target insects.