Understanding the processes controlling organic matter (OM) stocks in upland soils, and the ability to management them, is crucial for maintaining soil fertility and carbon (C) storage as well as projecting change with time. OM inputs are balanced by the mineralization (oxidation) rate, with the difference determining whether the system is aggrading, degrading or at equilibrium with reference to its C storage. In upland soils, it is well recognized that the rate and extent of OM mineralization is affected by climatic factors (particularly temperature and rainfall) in combination with OM chemistry, mineral–organic associations, and physical protection. Here we examine evidence for the existence of persistent anaerobic microsites in upland soils and their effect on microbially mediated OM mineralization rates. We corroborate long-standing assumptions that residence times of OM tend to be greater in soil domains with limited oxygen supply (aggregates or peds). Moreover, the particularly long residence times of reduced organic compounds (e.g., aliphatics) are consistent with thermodynamic constraints on their oxidation under anaerobic conditions. Incorporating (i) pore length and connectivity governing oxygen diffusion rates (and thus oxygen supply) with (ii) ‘hot spots’ of microbial OM decomposition (and thus oxygen consumption), and (iii) kinetic and thermodynamic constraints on OM metabolism under anaerobic conditions will thus improve conceptual and numerical models of C cycling in upland soils. We conclude that constraints on microbial metabolism induced by oxygen limitations act as a largely unrecognized and greatly underestimated control on overall rates of C oxidation in upland soils.