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A nine-year nitrogen addition experiment in a poplar plantation reveals a critical hidden risk: N deposition destabilizes subsurface (10–20 cm) soil carbon by shifting it from stable mineral-associated (MAOC) to vulnerable particulate (POC) forms. This repartitioning is driven by stoichiometric imbalances that suppress microbial carbon use efficiency and reduce microbial necromass production, weakening the “microbial carbon pump”. Surface soils (0–10 cm) remain buffered by continuous litter inputs. This challenges current sequestration estimates by revealing overestimated long-term stability, thus necessitating the integration of soil carbon fractions and vertical stratification into global climate models.