<p>Agroforestry landscapes in East Africa are highly heterogeneous, and their contribution to ecosystem services, particularly carbon storage, remains poorly understood. This study examined the drivers of aboveground carbon stocks in smallholder agroforestry systems in the Eastern Province of Rwanda, where agroforestry has been promoted as a restoration strategy. Average carbon stocks were low (1.02 ± 1.50&#xa0;Mg C ha⁻¹) but varied substantially within and among the four landscapes sampled. Plot-level characteristics related to soil depth and slope were significantly associated with higher carbon stocks, suggesting that these strata may act as proxies for multiple underlying physical processes that regulate carbon storage. Climatic factors showed mixed effects: mean annual temperature was positively associated with predicted carbon stocks (<i>p</i> &lt; 0.001), whereas the positive effect of mean annual precipitation was not statistically significant (<i>p</i> = 0.06). Tree density had a significant positive effect on aboveground carbon stocks (<i>p</i> &lt; 0.001), and the interaction between native tree abundance and spatial configuration was also positively associated with carbon stocks (<i>p</i> &lt; 0.001). Maximum diameter at breast height (DBH), used as a proxy for tree size, had a strong positive effect, highlighting the importance of conserving large trees to enhance carbon sequestration. Our findings underscore the value of integrating carbon stock assessments into climate-smart agroforestry management and promoting native tree species to enhance carbon sequestration in intensively farmed smallholder landscapes.</p>