We analysed a large dataset consisting of 457 soil profiles of Andisols and Ultisols of volcanic origin compared to 60 non-volcanic soils. We hypothesised that soil pH has a greater impact on the development of Al-organomineral complexes in volcanic soils compared to non-volcanic soils, in the latter, the silt and clay fractions play a crucial role. Soil pH >4.5 strongly influenced the formation of Al-organomineral complexes in volcanic soils, while an increase in allophane content led to a decrease in SOC. Ultisols with more crystalline clays, such as halloysite and disordered kaolinite, the pH had a weaker impact and there was no effect on non-volcanic soils. Instead, a positive correlation (R2 = 0.63, p < 0.01) was found between silt and clay and SOC in non-volcanic soils, supporting our second hypothesis. Soil pH played a significant role in the interplay between Al-organomineral complexes and allophane formation, while crystalline mineralogy has a direct effect on SOC levels in non-volcanic soils.