The reuse of biogas effluent (BE) represents a sustainable approach for nutrient recycling in agricultural systems, particularly in regions with intensive livestock production. However, its application is often limited by low nutrient concentrations and inefficient management based on total nitrogen content. This study evaluated the effects of BE applied at different ammonium nitrogen (NH₄⁺–N) levels (BE-100, BE-150, BE-200) on rice growth, yield, and nitrogen use efficiency under mesocosm conditions, in comparison with synthetic fertilizer (SF-150) and a no-nitrogen control (Ze-N). Results showed that BE significantly improved plant growth and yield, with grain yield increasing from 513 g m⁻² in the control to 826–898 g m⁻² in fertilized treatments. The highest yield was observed in BE-200 level, comparable to synthetic fertilizer application. Yield improvements were mainly associated with increased panicle length and spikelets per panicle, while other components showed no significant differences. Nitrogen uptake increased under all fertilized treatments, whereas nitrogen use efficiency did not differ significantly. The findings indicate that NH₄⁺–N-based management of BE can maintain rice yield while reducing the effluent volume required. This approach enhances nutrient recycling efficiency and contributes to environmentally sustainable agricultural practices. A key novelty of this study is the development of an NH₄⁺–N-based application strategy that enables farmers to estimate the appropriate BE application rate using simple NH₄⁺ test kits, thereby facilitating field-scale adoption, reducing excessive wastewater use, and promoting sustainable and biosafe recycling of livestock waste in rice production systems. The results provide practical insights for improving the application of biogas effluent in rice-based systems while reducing the environmental risks associated with excessive effluent application.