The mechanisms by which lime and/or phosphate addition impacts the preservation of soil organic matter (OM) are poorly understood. We explored the changes in quantity and chemistry of water-extractable organic matter (WEOM) in the bulk soil and its heavy density fraction (>1.6 g/cm3) of an unmanaged C-rich volcanic soil caused by lime and/or phosphate application. The addition of lime or phosphate caused (i) a significant increase in the WEOM, along with a decrease in its C/N ratio and an increase in its aromaticity, and (ii) changes in the WEOM chemical composition, measured with pyrolysis-gas chromatography/mass spectrometry, this being most impacted by lime application. The combined effect of lime and phosphate addition on the quantity and chemistry of WEOM was larger than the effects of separate lime and phosphate additions. By comparing the response of the bulk soil and the heavy fraction, we infer that phosphate has a greater contribution to the destabilization of vulnerable particulate OM, while lime causes a comparable disruption in the particulate OM and that in the heavy fraction. These findings provide a mechanistic insight into the decreased OM stability after liming and/or P fertilizing Andosols. They have implications for designing climate-smart management practices for these soils.