In Peruvian Amazonia, cropping techniques manipulating the biological processes of soil fertility have been tested to increase productivity and sustainability of crops. Special attention was paid to earthworms since their communities are dominant in natural ecosystems and severely depleted in cultivated soils, and also because their populations can be manipulated. The objective of this work was to evaluate the impact of the endogeic earthworm Pontoscolex corethrurus on soil organic matter dynamics, by comparing treatments with and without earthworms. Carbon dynamics is described using particle-size fractionation and in situ natural isotopic labelling (carbon 13) obtained by shift of C3 to C4 vegetation. After 6 years of maize cultivation, the organic carbon stock of the 0–10 cm layer decreased respectively by 4 and 27% in the control and the earthworm inoculated treatments. For the inoculated treatment this decrease mainly occurred in the large particle size (plant residues). Seventy % of the carbon derived from forest was lost during 6 years in the 2000–200 μm fractions in the inoculated treatment and 19% in the control. However, the incorporation of carbon derived from maize in soil, especially in the large particle fractions (>50 μm), was lower in the earthworm inoculated treatment. Accordingly, the proportions of carbon derived from forest and from maize were the same in the two treatments. Thus, the main effect of earthworm inoculation was a more important mineralisation of the carbon derived from forest and maize, especially in the large particle size fractions (>50 μm).