Purpose <p>The influence of nitrate on methane production has been widely studied, but few studies have focused on the co-contamination between nitrate and other pollutants on methane production in paddy soil.</p> Materials and methods <p>Paddy soil samples (Guangdong province, China) were spiked with nitrate at three concentrations (200, 500, 1000&#xa0;mg/kg) in the presence of Cr (VI). Batch incubations under anaerobic conditions (35&#xa0;days) monitored methane, CO₂, other environmental factors, and Microbial community.</p> Results and discussion <p>The results revealed that nitrate exerted a complex impact on microbial processes. Specifically, the presence of nitrate resulted in a 12% and 45% reduction in cumulative methane production for the N500 and N1000 groups, respectively, compared with the control. Simultaneously, nitrate promoted the decomposition of organic matter, production of CO₂ and reduction of Fe (III). Notably, it was observed that nitrate have a significant promotion on the growth of hydrogenotrophic methanogens, such as <i>Methanobacterium</i> and <i>Methanocella</i>. Furthermore, nitrate significantly promoted the proliferation of fermentative Fe (III)-reducing bacteria like <i>Clostridium</i> and <i>Thermincola</i>. Redundancy analysis (RDA) revealed a positive correlation between fermentative Fe (III)-reducing bacteria (<i>Clostridium</i>) and Cr (VI) levels, indicating that these bacteria may reduce Cr (VI) to the less toxic Cr (III), leading to a significant decline of Cr (VI) during the early period.</p> Conclusion <p>Nitrate inhibited methane production while boosting CO₂ production and Cr (VI) reduction in paddy soil. This work may provide valuable insights into microbial cooperation and competition in paddy soil, aiding efforts to reduce methane emissions.</p>