The stability of soil organic matter (OM) in Amazonian anthropogenic soils, Terra Preta de Índio (TPI), is still not completely understood. The large contribution from black carbon (BC) and minerals to these soils is well-known; OM stability is therefore frequently explained by these properties, providing intrinsic recalcitrance (BC) and chemical protection against decomposition (OM-mineral associations), but the relative importance of both mechanisms that underlie the stability are not yet understood. In order to better understand the sources and decay processes of soil OM in these soils, we studied the molecular composition using pyrolysis gas-chromatography/mass-spectrometry. To this end, several soil OM fractions of samples from two TPI soils and an adjacent Xanthic Acrisol that served as a reference soil (REF) were studied (0–2 m depth). A sequential fractionation was applied in order to better understand the composition of soil OM pools with different association to the soil matrix. The studied soil OM fractions included the free light fraction (FLF; i.e., charcoal and litter), the occluded light fraction (OLF; charcoal and litter within aggregates), 0.1 M NaOH extractable OM (EX; comparable with the combined humic acid and fulvic acid fractions), and the remaining residue (RES; treated with HF/HCl; comparable with the humin fraction). The largest contribution to the total soil OM was found for EX and/or RES, the sum of which varied between 79% and 98% (Ave. 90.8%, n = 18). The minor contribution from the OLF (Ave. 4.4%) indicates that stabilisation within aggregates was not a major factor that contributed to OM stability in the studied profiles. Differences in molecular composition between the fractions were larger than those between profiles or with depth. The EX fraction showed the lowest contribution from plant (lignin phenols) and BC (PAHs, indenes, aromatics) derived products. The RES fraction showed a significantly larger contribution from BC related pyrolysis products compared to the EX. This non-extractable BC that is present in the RES after removal of the light fractions may reflect preferential binding of PAHs to minerals or, alternatively, the presence of highly condensed macromolecular polyaromatic structures. Changes with depth within the EX and RES fractions showed a larger contribution from products derived from BC in the anthropogenic horizons. Furthermore, the OM composition in EX and RES indicated that the degree of degradation of OM in anthropogenic horizons was relatively low. Apart from these similarities for anthropogenic horizons, the chemical composition of soil OM also showed large differences between both TPI soils. TPI-1 showed large variation between horizons while TPI-2 showed only minor changes with depth; this may be related to different phases of human occupation with time and/or a different soil usage.