Microbially-incorporated heavy metals have not been studied enough in spite of their importance in phytoremediation. Heavy metals contained in microorganisms can be released easily into soil after cell death, which in turn contributes to an increased efficiency in phytoextraction. The present study aimed to quantify microbially-incorporated heavy metals in response to amendment of green manure and inorganic fertilizers in heavy metal contaminated soils. In lightly contaminated soils, microbial biomass increased steadily through out the growing season of celery and had strong positive correlation with photosynthetic CO2 uptake, soil respiration, root biomass. Rye-amended soils showed marked higher microbial biomass than inorganic fertilizer-amended soils. In addition, this enhancement in microbial population corresponded to application dose. On the other hand, in heavily contaminated soils, microbial biomass declined consistently with time, which was largely attributed to increased free or exchangeable heavy metals, and to increased soil acidity during the growing season. Heavy metals incorporated in microbial cells, which was quantified with a chloroform fumigation and extraction method, revealed that the microbial heavy metal portions, in case of Cd and Cu, accounted around 1 to 5% of total and 5 to 20% of labile pool, respectively. Generally, Cd was more likey to be incorporated into microbial cells. Heavy metal contents in microorganism had positive correlations with plant biomass, soil respiration, and microbial biomass. Interestingly, exchangeable heavy metal pools were negatively correlated with microbial heavy metal pools, which implies some portion of exchangeable heavy metal was consumed by soil microorganisms. Futhermore, those microbially-incorporated heavy metal pools had significantly positive association with heavy metals removed by plant. Therefore, our finding strongly suggests regulation microbial pool of heavy metal can be an important control in phytoremediation of heavy metal contaminated soils.