Optimising the efficiency of applied nitrogen (N) fertilisers is essential to sustain agricultural systems. Substantial N losses continue through leaching, volatilisation, and denitrification processes. Co-application of organic amendments and biochar alongside synthetic fertilisers is a widely practiced strategy to enhance N retention, improve soil fertility and increase crop productivity. Previous studies have focused on the specific characteristics of soil amendments and the magnitude of yield change, while N use efficiency (NUE) and economic returns remain uncertain. This meta-analysis examined the effects of synthetic fertiliser applied alone, co-applied with biochar and co-applied with organic amendments, on crop yield, plant N uptake, NUE and economic return within rice cropping systems. Synthetic fertiliser and biochar applied alone increased rice yield by 69.2% ± 30.3 and 33.4% ± 34.9, respectively (Bootstrap 95% CI), whereas yield further increased by co-applying biochar (+104.8% ± 37.5) and organic amendments (+80.2% ± 18.2) with fertiliser compared with non-fertilised control. Co-applying organic amendments (+20.9% ± 29.7) and co-applying biochar (+35.1% ± 18.3) with synthetic fertiliser increased NUE compared with fertilised control. For rice crops under low N application (< 150 kg ha−1), co-applying biochar with fertiliser increased yields more than co-applying organic amendments (+70.1% ± 0.7 vs. +52.5% ± 0.3, respectively). Within acidic soils, co-applying biochar with fertiliser (+72.9% ± 0.4) led to higher yield than co-applying organic matter (+36.0% ± 0.9), and among soils with high organic carbon concentration, co-applying biochar with fertiliser increased yield by 97.6% ± 1.6, compared with yield increases observed by co-applying organic matter with fertiliser at 29.4% ± 0.5 and fertiliser alone at 25.6% ± 0.2. The main factors driving rice yield were N application rate, co-application method and soil organic carbon concentration. Co-applying either biochar or organic amendments did not significantly differ in benefit–cost ratio with benefit–cost ratios of 35.1% ± 9.2 and 18.1 ± 26.5, respectively compared with fertilised control. Co-applying either biochar or organic amendments with synthetic fertilisers decreased N inputs and increased economic return, therefore improving sustainability in rice cropping systems.