Soil organic C (SOC) stock in tropical forests can be reduced significantly after logging, not only due to lowered above ground biomass (AGB) and consequentially reduced organic matter (OM) input, but also consumption on sequestrated soil C protected by OM-mineral association. In this study, we studied the loss of mineral-associated OM after logging in the main rooting zone (e.g., 0–30 cm), and examined a hypothetical twofold underlying mechanism of SOC reduction: first, decrease in AGB limiting OM input; second, decrease in soil redox potential (Eh) leading to the reductive dissolution of short-range-ordered iron (SRO Fe) minerals that destabilize some mineral-associated OM. Thirty-five plots at different degradation levels were investigated for both above- and belowground properties. AGB and tree community composition were employed as indicators of forest degradation gradient; multiple physicochemical properties in top-30 cm soils were measured every 10 cm depth. We analysed the relationship between AGB and soil C with the mediator SRO Fe, and investigated the role of soil Eh in linking the changes in AGB and SRO Fe. Our results revealed simultaneous decreases in AGB, SRO Fe and soil C in top-30 cm soils, and SRO Fe mediated 43 % of the hypothetical causal effect of AGB on soil C in deeper (20–30 cm) soil. Soil Eh decreased with decreasing AGB in a logistic pattern, dropping to a reductive regime (Eh7 ≤ 0.05 V) when more than half of the AGB was removed from the pristine level. Mean SRO Fe stock in the reductive soils was significantly lower than that in the oxic soils (Eh7 > 0.05 V), and the loss of SRO Fe correspond to the decomposition of OM in 10–30 cm soils. We suggest that the reductive shift in soil is caused by the weakened evapotranspiration as destructive selective logging inflicts canopy openness and succession failure. This study presents the possibility that forest degradation may reduce the size of protected soil C pool resulting from the loss of soil SRO Fe minerals.