Within agroforestry systems, trees greatly contribute to soil carbon (C) sequestration. We still know little about how this contribution varies according to tree species. Here, we quantified the soil C content derived from three main tree species, Eucalyptus robusta, Coffea arabica and Citrus clementina, used in rainfed rice-based agroforestry in the Highlands of Madagascar. A fully factorial controlled mesocosm experiment was performed, with seedlings of the tree species planted with or without rice in a Ferralsol. The natural 13C abundance in the soil was measured to assess tree- and rice-derived C. One year after planting, Eucalyptus robusta was the species exhibiting the highest tree-derived C values, with 148 g C m-2 on average. In contrast, Citrus clementina transferred only 12 g C m-2 to the soil. No significant contribution of Coffea arabica to the soil C stock was found. The presence of rice affected neither the growth of tree seedlings nor their abilities to provide C to the soil. The difference in soil C sequestration among tree species was significantly correlated with differential root biomass. Tree root biomass was significantly correlated with soil d13C. This experimental assay highlighted the contrasting contributions of tree species to ecological processes such as soil C sequestration at the early stage of agroforestry establishment. Further studies considering tree density and spatial arrangement should be conducted under field conditions to gain further insights into tree contributions to soil C sequestration in agroforestry systems.