The organic carbon of particle size <53 μm is mineral-associated organic carbon (MAOC), the measurable fraction of passive soil organic matter pool described in CENTURY model. We studied the effect of fresh organic matters (FOMs): no OM (control); chicken manure (CM): 2.12 g CM carbon kg−1; and leaf litter (LL): 1.81 g LL carbon kg−1 on short-term dynamics of MAOC and CO2 evolution of two soils: Bagabag, Philippines (121°15′E, 16°35′N) and Tsumagoi, Japan (138°30′E, 36°30′N). Cumulative CO2 evolution was significantly higher in CM-applied soils. Significant MAOC decrease in 5–20-cm depth of Tsumagoi soil suggest short-term stable C turnover even with FOM application. Greater MAOC decline in CM-applied Bagabag soil suggest that manure application may result to bigger stable C turnover in this soil. Our results provide evidence of significant short-term stable SOC turnover, and challenge the convention that only labile SOC is involved in short-term CO2 evolution from soils.