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Land use changes (LUC) for the expansion of bioenergy cropping have caused consistent reductions in soil organic carbon (SOC) stocks in tropical soils. This study addresses the mechanisms underlying such SOC losses by assessing LUC effects on, and relationships between, soil engineering invertebrate fauna, soil structural stability, and C allocation and sequestration within soil aggregates. We sampled three sites with sets of land use types varying in the level of anthropogenic stress in sandy loam, sand clay loam, and clay soils along a 1000-km-long transect in central Brazil, where bioenergy cropping expands across pasturelands. We quantified the effects of LUC on soil engineer fauna (i.e., termites, earthworms, coleopterans, and ants), soil structural stability, and C allocation and fitted structural equation models (SEM) to elucidate mechanistic links between the measured variables. We found that reductions in SOC stocks following LUC were concomitant with reductions in the abundance of soil engineers (log abundance of soil engineers, −1.17 ± 0.54; P = 0.0322), destabilization of soil structure (normalized stability index, −0.16 ± 0.04; P < 0.0001), and soil depth-dependent decreases in the amounts and increases in the humification degree of aggregate-occluded SOC. Our SEMsupported the predicted relationships among these responses, and indicated that soil engineering by invertebrates indirectly mediated changes in SOC stocks across land uses by controlling the physical protection of low-humified, aggregate-occluded SOC, a C fraction that accounted for over 90% of the change in total SOC stocks following LUC. When analysing the influence of the different invertebrate groups separately, we found stronger support for the role of termites in this process compared to that of earthworms, coleopterans, and ants. Hence, negative LUC effects on populations of soil engineers weaken soil functioning and its C storage. These results highlight the need for land-use strategies that maintain soil fauna in order to sustain key ecosystem processes like soil structural formation and soil C stabilization. • Soil engineering by invertebrates indirectly mediated changes in SOC stocks following land-use change (LUC). • Invertebrates control the physical protection of low-humified, aggregate-occluded SOC. • Microaggregate-occluded SOC can account for over 90% of the change in total SOC stocks following LUC. • Termites can have a more prominent role in this process compared to earthworms, coleopterans, and ants. • Negative LUC effects on populations of soil engineers weaken soil functioning and its C storage. [ABSTRACT FROM AUTHOR]