The existing information on soil carbon (C) stabilisation in allophanic soils is conflicting because active Al3+ and sesquioxides (i.e., the oxides/hydroxides of Al and Fe) as a stabilising agent of soil C are emphasised in opposition to allophane and imogolite type materials. Two hypotheses were tested in this study: 1) Al (and Fe) complexed with soil C and allophane content are the key variables to explain the soil C level in Chilean allophanic soils, and 2) the existing metal–SOM complex and short-range ordered aluminosilicate minerals in allophanic soils mainly result from soil pH variation and competition between Al (and Fe) for SOM and allophane formation. This study established the relationship among different soil properties such Al-, Fe-complexes and allophane content on soil C levels in Chilean volcanic soils as well as the effect of soil pH on metal–OM complexes. A total of 45 soil samples from 15 soil pedons were sampled at 0–0.1, 0.1–0.2 and 0–2–0.4 m. The soil samples were analysed for the content of soil organic C, allophane, clay, silt and Na- pyrophosphate extraction (Alp, Fep, Cp) and soil pH (water). We examined the relationship between the soil C content and soil properties using simple and multiple linear regressions. The silt and clay contents explained little, while the allophane, soil pH and Alp explained most of the soil C variation. We found an inverse relationship between soil pH and Alp (and Fep), indicating that the soil pH was significantly correlated with Alp and Fep, while the allophane content was positively related with soil pH. The results also showed a higher atomic ratio (Al+ Fe)p:Cp in deep (0.2–0.4 m) horizons; the opposite was true in the top soil horizon (0–0.1 m), supporting the idea that SOM in deep soils is saturated with Al and Fe, leaving extra metal to react with silica for allophane formation.