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Volcanic ash soils display distinctive morphological, physical and chemical properties and they contain several times more organic matter than non-volcanic soils. So far, there are few studies of soil organic matter (SOM) distribution in different chemically and physically protected carbon pools of soil horizons of volcanic soils. The aim of this study was to determine the SOM distribution (and its δ13C and δ15N composition) in different chemical and physical fractions at various depth horizons of two Andisols under pasture or rain forest in southern Chile. We used the amount of humus-complexes (Cp) extracted with Na pyrophosphate as a measure of C stabilized by aluminum (Alp) and iron (Fep) in combination with density fractionation to separate particulate organic matter as free (fPOM), occluded (oPOM) and organic matter associated with the mineral fraction (MF). The results showed that soil SOM stock (0–40 cm) in the pasture soil was 166 Mg C ha−1 (11.7 Mg N ha−1) and in the forest soil 100 Mg C ha−1 (4.1 Mg N ha−1). The SOM variation was explained largely by the differences in Cp, Alp and Fep. About 34% of total soil C was found as Cp in both oPOM and MF in the topsoil, whereas 33–53% was found in the subsoil horizons. The oPOM fraction was more important in the forest soil and generally decreased in the subsoil where these fractions were enriched with δ13C and δ15N. Our results emphasize the importance of the humus complex and oPOM formation as the SOM stabilization mechanism in the forest Andisol, whereas under pasture organo-mineral interaction, including the formation of humic-metal complexes, is the most important stabilization mechanism. A conceptual model is lacking to demonstrate the major areas of uncertainty within known mechanisms and factors that explain the distribution of SOM through soil profiles in Andisols.