AbstractSoil respiration, resulting in decomposition of soil organic carbon (SOC), emits CO₂ to the atmosphere and increases under climate warming. However, the impact of heavy metal pollution on soil respiration in croplands is not well understood. Here we show significantly increased soil respiration and efflux of both CO₂ and CH₄ with a concomitant reduction in SOC storage from a metal polluted rice soil in China. This change is linked to a decline in soil aggregation, in microbial abundance and in fungal dominance. The carbon release is presumably driven by changes in carbon cycling occurring in the stressed soil microbial community with heavy metal pollution in the soil. The pollution-induced increase in soil respiration and loss of SOC storage will likely counteract efforts to increase SOC sequestration in rice paddies for climate change mitigation.