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Biogas digestive effluent (BDE) is a nutrient-enriched source that can be utilized as an organic fertilizer for rice cultivation without synthetic fertilizer (SF) application. However, a primary concern is the stimulation of methane (CH₄) emissions due to the enrichment of the labile organic carbon, a favorite substrate of methanogenic archaea. Methanotrophs potentially reduce greenhouse gas (GHG) emissions from rice fields owing to metabolizing CH₄ as a carbon source and energy. We therefore examined the effect of the application of methanotroph-inoculated BDE to the rice cultivated paddy soil on GHG emissions and rice productivity under a pot experiment. Methanotrophs (<i>Methylosinus</i> sp. and <i>Methylocystis</i> sp.), isolated from the Vietnamese Mekong Delta’s rice fields, were separately inoculated to the heated BDE, followed by a 5-day preincubation. Methanotroph-inoculated BDE was supplied to rice cultivation to substitute SF at 50% or 100% in terms of nitrogen amount. The results showed that the total CH₄ emissions increased ~34% with the application of BDE. CH₄ emissions were significantly reduced by ~17–21% and ~28–44% under the application of methanotroph-inoculated BDE at 100% and 50%, respectively. The reduction in CH₄ was commensurate with the augmentation of <i>pmo</i>A transcript copy number under methanotroph-inoculated BDE. In addition, methanotroph-inoculated BDE application did not increase nitrous oxide (N₂O) emissions and adversely affect rice growth and grain productivity. This study highlighted the BDE-recirculated feasibility for a lower CH₄ emission rice production based on methanotrophs where high CH₄-emitting fields were confirmed.