To investigate both the effect of land-use systems on SOM characteristics and the effect of occlusion in aggregates on chemical composition of the occluded fraction, SOM fractions of soils under Cerrado, no-tillage and conventional tillage, were investigated. Free light, occluded light and extractable organic matter from native Cerrado and from tilled and untilled fields under maize and bean rotation were separated and chemically analysed by pyrolysis-GC/MS. Ploughing incorporated more fresh OM into the soil than natural biological activity. Degradation of the occluded light fraction was not fully halted, but was different from that of SOM in the extractable fraction. Recalcitrant compounds had low abundances in the free light and extracted fractions, but were more abundant in the occluded light fraction, where the more accessible compounds were depleted by microbial decomposition. Because of intense decomposition, the extracted fractions did not differentiate between land uses, but differences in the light fractions were significant. The results indicate that the decay of the occluded fraction is different from that of the free light fraction: non-ideal circumstances of decay caused a relative accumulation of potentially recalcitrant compounds. When considering the rapid turnover of all components in the soil extracts, disruption of aggregates will probably cause rapid decay of the occluded fraction. The distribution of pyrolysis products that can be ascribed to charred wood (polyaromatics) indicates that this fraction is readily decayed if not occluded. Selective decomposition in the occluded fraction may cause a shift in δ13C that should not be misinterpreted.