The effect of organic amendment on the resistance and resilience of the organic matter decomposing activity was compared between soils amended with compost and with chemical fertilizers. The impact of metam sodium disinfection on cellulose‐decomposing activity and on the number of nematodes in three types of soils was periodically measured. In an andosol, cellulose‐decomposing activity was significantly suppressed by soil disinfection only in the chemically fertilized soil (CF‐soil) and not in the soils to which cow manure compost and okara (the residue in tofu production)/coffee compost was added. In a brown lowland soil, cellulose‐decomposing activity was significantly suppressed by soil disinfection in the CF‐soil, but not in the soils to which higher amounts of cow manure compost and pig manure compost had been added. In a red‐yellow soil, cellulose‐decomposing activity was significantly suppressed by soil disinfection in all soils, but its resilience was higher in the soils to which cow manure compost or coffee compost was added compared with the CF‐soil. Total numbers of nematodes were markedly decreased by soil disinfection in all soils. These results may suggest that the resistance and resilience of cellulose‐decomposing activity against soil disinfection were enhanced by organic amendments, while disinfection had fatal effects on soil nematodes. In most of the organically amended soils, the mean weight diameters of aggregates were larger compared with the CF‐soils, suggesting that highly structured soil pore networks may provide shelters for the soil microbes responsible for cellulose decomposition against disinfection. This hypothesis was supported by the result that the resistance of cellulose‐decomposing activity against soil disinfection decreased when the soil structure was destroyed by grinding in a mortal and pestle.