<p><strong>Background</strong>. Soil aggregates represent a major indicator of soil fertility as they are important components of soil C protection. However, in the Democratic Republic of Congo, the choice of tree species being integrated into crop farms influence the type of soil macrofauna beneath these agroforestry trees with effect on soil aggregates and carbon fractions. <strong>Objective</strong>. To assess the combined effect of diverse tree species alongside earthworms and termites on soil aggregation and soil organic C. <strong>Methodology</strong>. Soil samples were collected from five agroforestry systems comprising <em>Eucalyptus saligna,</em> <em>Grevillea robusta</em> and <em>Ficus benghalensis</em> (an indigenous tree) woodlots, an agricultural farm (beans) and a natural forest in four different locations. Soil aggregates and soil organic C were analysed in the laboratory following standard procedures. The analyses of variance and correlations were carried out using R programming software. <strong>Results</strong>. A significantly higher proportion of large macroaggregates was recorded in soil under natural forest (13.1 %) whereas microaggregates were significantly low in soils under natural forest. For all the categories of aggregate-associated C, natural forest recorded the highest values while beans had the lowest values. The same trends were observed for labile C with 22.9 g kg<sup>-1</sup> in soil under natural forest and 9.7 g kg<sup>-1</sup> in soil under beans. <strong>Implication</strong>. The high levels of soil aggregates as well as carbon fractions recovered from natural forest clearly show the significance of a well-diversified tree-based farm. <strong>Conclusion</strong>. Therefore, it is advisable to consider a large diversification of tree species on farms to sustain and maintain a better soil quality.</p>