A paddy soil, with microbial biomass considerably reduced by chloroform fumigation, was treated with low-crystalline ferrihydrite and high-crystalline goethite and with 13C-labeled acetate. In the first 10 days of the incubation, CH4 was produced mainly from the added acetate (56‒91%). After day 30, however, 3‒11% of the total CH4 emissions originated from the added acetate. Chloroform fumigation reduced the microbial biomass by 43‒87%, leading to the decrease in the CH4 emission from the fumigated soil for 352‒1127 times compared to that from the unfumigated soil. Acetate only contributed to 0‒6% of the total CH4 emission from the fumigated soil during the entire incubation period. Thus, chloroform fumigation largely reduced the abundance of methanogens, and the reduction in the abundance of acetotrophic methanogens was high. Iron oxide additions reduced CH4 emissions from the added acetate and from other sources. The reduction was stronger in the fumigated soil compared to that in the unfumigated soil because the lower abundance of methanogens in the fumigated soil decreased the competition for substrates with iron reducers. The effect of ferrihydrite on CH4 emission from non-acetate sources was stronger than that of goethite before day 6; however, this effect became weaker thereafter, because of the reduced number of reactive sites after acetate sorption by ferrihydrite. We conclude that the marked reduction in the microbial biomass, and especially methanogens, decreased the methane production, changed the CH4 sources, and increased the relative effects of iron oxides on CH4 production. © 2022, The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.