Methane oxidation coupled to sulfate reduction is the dominant process restricting methane release from cold seeps. Methane oxidation can also be coupled to nitrate/nitrite reduction, thereby linking the cycles of three major greenhouse gases. Yet, how this coupling shifts during seep development and its impact on N₂O production remain poorly understood. Here, we integrated geochemical profiling, ¹⁴C-based labeling, and omics-based analyses to quantify process rates, identify key microbial mediators, and assess net N₂O productions across development stages of cold seeps in the South China Sea. In an early-stage, polychaete-dominated seep, depth-integrated potential nitrate/nitrite-coupled methane oxidation rate reached 21.9 ± 3.0 mmol C/m²/d, accounting for 36–73% of the total methane oxidation. By contrast, in a typical epifauna-prevalent mature seep, this contribution diminished to ~1% (0.62 ± 0.16 mmol C/m²/d) while sulfate-dependent methane oxidation became dominant. Omics data identified the predominant methane-oxidizing bacteria Methyloprofundus and QPIN01 (relative abundances of 7–24%), as the potential mediators of nitrate/nitrite-coupled methane oxidation in the early-stage seep sediments. Consistent with the absence of N₂O-reduction gene nosZ in these lineages, simultaneous nitrate and methane amendments significantly stimulated net N₂O production by 14–46% in the early-stage seep sediments. This increase correlated strongly with the potential nitrate/nitrite-coupled methane oxidation rate and was estimated to offset 41 ± 9% of the climate benefit gained through methane oxidation. These findings revealed the previously unrecognized successional dynamics of dominant methane oxidation pathways and necessitate the incorporation of nitrate/nitrite-coupled methane oxidation into assessments of greenhouse-gas release from these globally relevant ecosystems.

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