The combined effects of tillage and organic amendments on microbial respiration and its contribution to soil hydraulic conductivity are still uncertain in the 0–40 cm layer of a loess soil. We conducted a two-year field experiment to explore the effects of organic amendments, tillage and their interaction on soil microbial respiration, aggregate stability, pore parameters, and hydraulic conductivity on the Loess Plateau. Three tillage methods (conventional tillage (CT), deep tillage (DT) and no tillage (NT)) plus five fertilizer treatments (mineral fertilizer (control) alone and along with 20 t ha⁻¹ wheat straw (MWS), wheat husk (MWH), farmyard soil (MFS) and bioorganic fertilizer (MBF)) were set up as experimental treatments. The findings demonstrated that the organic amendments significantly increased the soil microbial respiration and saturated hydraulic conductivity compared to the control in the 0–10 cm and 10–20 cm layers. Soil microbial respiration had indirect effects on hydraulic conductivity by improving the water aggregate stability and macroporosity. Additionally, the interaction effects of tillage and organic amendments on the pore and hydrological parameters were significant in the 20–40 cm layer. NT-MBF resulted in the greatest saturated hydraulic conductivity, which was directly correlated with the soil’s strong pore organization. Given the issue of subsurface soil compaction in our study area, it is recommended that local farmers adopt NT-MBF to enhance the soil’s microbial, structural and hydrological properties.

Controversy persists on a global scale regarding the trade-offs between greenhouse gas (GHG) emissions, yield, the global warming potential (GWP), and GHG intensity (GHGI) following organic fertilizer substitution within vegetable cropping systems. This study aimed to quantify these effects under diverse conditions and elucidate the direct and indirect drivers governing these outcomes through a meta-analysis and structural equation modeling (SEM). We synthesized 655 paired observations from 69 published studies using random-effects meta-analysis, finding that organic fertilizer substitution significantly increased CH₄ emissions and GWP compared to inorganic fertilizer controls. Although this was the general trend, organic fertilizer could reduce GWP under specific climatic and soil conditions by reducing N₂O emissions, such as mean annual precipitation <400 mm or soil total nitrogen ≥3 g kg⁻¹. These conditions were also associated with substantially higher yield and lower GHGI. Furthermore, SEM demonstrated that field management practices exerted significant direct effects on N₂O emissions, GWP, and GHGI. Reductions in N₂O emissions, GWP, and GHGI could be achieved with fertilizer application duration ≥10 years, total N application rate ≥300 kg ha⁻¹, and field cultivation or plowing. GHGI was also reduced through yield enhancement under a moderate organic substitution rate (33–66%) or irrigation ≥300 mm. Our study provides a scientific basis for moving beyond universal recommendations towards precision organic management, which is essential for optimizing fertilization strategies to mitigate agricultural GHG emissions.