Liquid manure storage contributes substantially to environmental emissions within manure management systems. This study evaluated Yucca schidigera extract (YE) as a sustainable microbial modulator for mitigating ammonia (NH3) and greenhouse gas emissions during 60-day storage of liquid chicken manure. Three treatments were established: no additive (control, CK), 0.1% biological deodorant (positive control, BF), and 0.5% YE. The results demonstrated that both YE and BF significantly reduced electrical conductivity (EC) (YE: 38.35%; BF: 34.51%) and ammonium nitrogen (NH4⁺-N) content (YE: 14.15%; BF: 20.21%) relative to CK, while elevating the C/N ratio by 9.97% (YE) and 18.63% (BF). Total nitrogen decreased by 23.88% (YE) and 26.34% (BF) from initial levels. In addition, the cumulative NH3 emissions of YE and BF decreased significantly by 20.18% and 20.12% compared to CK. However, YE increased CH₄ emissions by 17.43%, elevating global warming potential, whereas BF exhibited no significant effect on CH4. Neither additive influenced CO2 or N2O emissions. Microbial analysis revealed YE enriched Firmicutes (e.g., Fermentimonas), while BF enhanced Actinobacteriota (e.g., Corynebacterium) and Proteobacteria. Both additives suppressed ammonia-producing bacteria (e.g., Proteiniphilum). Mantel tests analysis indicated NH3 emissions correlated positively with EC and NH4⁺-N (P < 0.01), while CH4 emissions correlated with organic matter (OM) content (P < 0.05). These findings elucidate the microbial mechanisms of YE in mitigating the NH3 emission during liquid manure storage, whereas YE may induce trade-offs in CH4 emission. In the future, the formulation of compound plant-derived additives will be necessary for the synergetic abatement of carbon and nitrogen gases.