Organic farming techniques in crop production are largely dependent on decomposition of the soil-amended organic matter (OM), which is naturally accompanied with release of greenhouse gases like as CO2, CH4, and N2O. In the present study, for soils amended with various OM (including compost, liquid organic fertilizer, and green manure), we have investigated emission fluxes of greenhouse gases and the concurrent changes in soil chemical properties and in soil microbial population. We also examined quantitative relationships between emission strengths and microbial populations. Generally, liquid biofiltrate and green manure including barley and hairy vetch showed highest emission strengths in both aerobic and anaerobic conditions. On the other hand, compost and inorganic fertilizers were considered to be relatively weak sources of GHGs. However, the integrated CO2 emission load for providing unit available N decreased in the order of barley, hairy vetch, compost, liquid biofiltrate, and inorganic fertilizer. Liquid biofiltrate and inorganic fertilizer were most efficient in providing available N, whereas compost was considered to be most appropriate for providing P with less emission of GHGs. We also observed a marked difference in microbial biomass among OM-amended treatments, which was well correlated with CO2 emission differences. In addition, through phospholipid fatty acid analyses, we found that distinct microbial populations were involved in decomposition of each OM. Especially, fungi played an important role in degrading large-size OM (e.g., green manure). The relative proportions of G(+)/G(-) bacteria and archea were associated with the relative easiness in degradation. On the other hand, CH4 emission fluxes were quantitatively correlated with the population size of methanogens for both incubation and field soils. The above results strongly suggest that both GHGs emision and nutrient availability must be taken into account to achieve the goals of organic farming and mitigating climate change. Futhermore, the observed quantitative relationships between GHGs emissions and microbial populations are expected to useful for examining various agroecosytems'' responses to OM management practices and future climate change sensories.