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Recycling of livestock manure in agroecosystems to partially substitute synthetic fertilizer nitrogen (N) input is recommended to alleviate the environmental degradation associated with synthetic N fertilization, which may also affect food security and soil greenhouse gas (GHG) emissions. However, how substituting livestock manure for synthetic N fertilizer affects crop productivity (crop yield; crop N uptake; N use efficiency), reactive N (Nr) losses (ammonia (NH3) emission, N leaching and runoff), GHG (methane, CH4; and nitrous oxide, N2O; carbon dioxide) emissions and soil organic carbon (SOC) sequestration in agroecosystems is not well understood. We conducted a global meta-analysis of 141 studies and found that substituting livestock manure for synthetic N fertilizer (with equivalent N rate) significantly increased crop yield by 4.4% and significantly decreased Nr losses via NH3 emission by 26.8%, N leaching by 28.9% and N runoff by 26.2%. Moreover, annual SOC sequestration was significantly increased by 699.6 and 401.4 kg C ha–1 yr–1 in upland and paddy fields, respectively; CH4 emission from paddy field was significantly increased by 41.2%, but no significant change of that was observed from upland field; N2O emission was not significantly affected by manure substitution in upland or paddy fields. In terms of net soil carbon balance, substituting manure for fertilizer increased carbon sink in upland field, but increased carbon source in paddy field. These results suggest that recycling of livestock manure in agroecosystems improves crop productivity, reduces Nr pollution and increases SOC storage. To attenuate the enhanced carbon source in paddy field, appropriate livestock manure management practices should be adopted.