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&NA; Previous studies showed that exoelectrogenic bacteria in paddy soil could suppress methanogens and methanogenesis after they were enriched by application of Fe3+ or running microbial fuel cells (MFCs). However, the relationship between exoelectrogenic bacteria and methanogens without the enrichment process is unknown. Our study was conducted in three paddy fields in China and over three seasons. We explored novel MFC‐based sensors to in situ detect voltage signals that were generated from paddy soil within 10 min. The voltage and methane emission flux were determined as an indicator of the exoelectrogenic activity and methanogenic activity, respectively. The abundance of exoelectrogenic bacteria was assessed by quantifying five exoelectrogenic bacterial‐associated genera including Geobacter, Shewanella, Anaeromyxobacter, Desulfovibrio and Clostridium, while the methanogens were studied by quantifying and sequencing the mcrA gene. The results showed that the abundance of exoelectrogenic bacteria and the voltage signals were positively correlated to the abundance of mcrA gene and methane emission flux, respectively. Moreover, non‐metric dimensional scaling reveals that the abundance of Geobacter, Desulfovibrio and Clostridium significantly correlated with that of Methanomassiliicoccus, Methanoregula and Methanolinea. The present study suggests that the voltage signals might act as a novel indicator of methane emission flux in paddy fields. &NA; Graphical Abstract Figure. The voltage signal of MFC sensors generated by soil exoelectrogenic bacteria might act as a novel indicator of methane emission flux in paddy fields.