Organic molecules from the soluble fraction of plant residues are less recalcitrant than macromolecules from plant cell walls such as lignins and cellulose. However, literature data suggests that the former may be stabilized in soil as much as the latter. We suggest that this is due to (i) diffusion of the soluble fraction in soil of the detritusphere and consequent protection from decomposition due to adsorption or entrapment in small pores and (i) rapid assimilation by the microbial biomass in the detritusphere, and consequent stabilization as recalcitrant or adsorbed microbial metabolites. We investigated these processes in soil microcosms using two approaches. First, we developed an new labelling method that specifically enriches in 13C the soluble fraction from plants, and analyzed the fate of this carbon in soil incubations. Second, we developed a meta-metabolomics approach by combining incubation of 13C labelled substrates with a non-biased analysis of the metabolites produced by or existing in bacterial cells by GC-C-IRMS.