Beef cattle production systems are the largest contributors of greenhouse gas (GHG) and ammonia (NH3) emissions in the livestock industry. Here, we present the first meta-analysis and integrated assessment of gaseous emissions and mitigation potentials for a typical beef cattle feedlot system, including methane (CH4), nitrous oxide (N2O), and NH3 losses from enteric fermentation and manure management based on data from 104 studies. A total of 14 integrated emission factors (EF) and the mitigation efficiencies (ME) of 17 available options were provided. The estimated GHG and NH3 emissions from the baseline feedlot system were 2786 ± 108 kg carbon dioxide equivalents (CO2-eq) per animal unit (AU) per year and 49.1 ± 1.5 kg NH3 AU-1 year-1, respectively. Enteric CH4 fermentation and manure on the feedlot contributed 67.5% and 80.8% of the total system GHG and NH3 emissions, respectively. The highest ME values were found for lipid additives for enteric CH4 fermentation and urease inhibitor additives (UI) for NH3 emissions from manure on the feedlot, being -14.9% ( p < 0.05) and -59.5% ( p < 0.001), respectively. The recommended mitigation combinations of a low-crude-protein (CP) diet and a UI additive for manure on the feedlot could reduce the GHG of the system by 4.9% and NH3 by 50.9%. The results of this study have important implications for developing sustainable beef cattle feedlot systems from the viewpoint of GHG and NH3 mitigation.