A Late Pleistocene to Holocene hydrosequence of podzols in the coastal plain of São Paulo (Brazil), of which the macromorphology was described previously, was investigated by pyrolysis‐gas chromatography/mass spectrometry (GC/MS). Differences in chemical composition of organic matter (OM) coincided very well with the morphological interpretation of these profiles with respect to drainage conditions, origin of OM, and decomposition. OM in B‐horizons of poorly‐drained profiles has a signature of dissolved organic matter (DOM), while that of well‐drained profiles indicates root‐derived material. Bands that, according to their morphology, were attributed to DOM have different signature within the profiles, reflecting DOM origin. The EB horizons of poorly‐drained profiles show a selective decay of B‐horizon material, resulting in a relative accumulation of aliphatics in poorly drained profiles. In the EB horizons of the well‐drained profiles, however, significant amounts of microbial products were accumulated and poly‐aromatic compounds were the most stable. This has not been described for temperate podzols. Factor analysis suggests that local differences in vegetation are responsible for about 50% of the total chemical variation in pyrolysates, whereas source, transport, and decomposition in the profile account for the other half. The results underline that OM composition of podzol horizons is strongly dependent on hydrological conditions, resulting in divergent soil organic matter (SOM) properties between soils from different landscape contexts. Nonetheless, there is a comprehensible relation between SOM fingerprints of horizons within one profile. Finally, changes in OM composition at horizon transitions provide insight into the podzolization process.