Amorphous mineral-associated organic carbon (AMAOC) and organo-Al/Fe complexes (Cp) play crucial roles in soil carbon (C) sequestration in volcanic soils. This study investigated the effects of land use management and liming on the C sequestration capacity of a young allophanic Andisol and old halloysitic-kaolinitic volcanic Ultisol sampled at 0–10 and 10–20 cm depth. This study was designed to test two hypotheses: (1) management and liming affect the C sequestration capacity of Andisol by reducing Cp and increasing AMAOC to offset Cp losses, and (2) they do not significantly affect the carbon sequestration capacity of Ultisol because of its more crystalline mineral forms and reduced amount of Cp. This study was conducted using a selective dissolution technique and density fractionation with agricultural soils and forests as control soils. After 43 years of intensive management and liming, the soil organic carbon (SOC) content decreased by 32% in the topsoil compared to the original native forest soil (178 ± 2 g kg−1 soil), mainly in the particulate organic matter (POM) fraction, which decreased by 74% compared to the native forest soil (61 ± 9 g kg−1 soil). However, Cp decreased only by 40% compared to the forest soil (62 ± 1 g kg−1 soil) from pHKCl 4.8–5.0, and AMAOC increased in 17% in the topsoil and 64% in the subsoil, supporting the first hypothesis of this study. In the cultivated Ultisol, SOC decreased by 35% due to the POM fraction, and mineral-associated organic C (MAOC) decreased by 37% compared to the forest soil (38 ± 7 g kg−1 soil). These results partially support the second hypothesis because the crystalline clay minerals from which MAOC originated remained unchanged and were strongly correlated with SOC. The mass balance of both soils indicated that the stable C losses from native forest soils were < 14%. These results highlight the importance of different C sequestration mechanisms to compensate for SOC losses in the young allophanic Andisol and old volcanic Ultisol. Our findings imply that both mechanisms can be used to estimate the C sequestration capcity in similar soil types.