Biochar-manure co-compost (BM) has garnered considerable attention as a promising soil amendment for improving nutrient retention and mitigating the emission of greenhouse gases (GHGs). However, its efficacy often varies largely from one soil to another. By comparing soil CO2 and N2O effluxes, solution chemistry, enzyme activities, and the abundances of N-cycle genes between BM and manure compost (M) across three soils of different texture classes through microcosm incubations, we aimed to develop biophysical mechanics to untangle the soil-dependent efficacy of BM in mediating soil carbon and nitrogen transformation processes. Compared to M addition, BM addition significantly reduced soil CO2 and N2O emissions, but its effectiveness was soil texture-dependent, being strongest for CO2 and N2O in fine-textured clay loam and coarse-textured sand, respectively. Such soil texture-dependent effects of BM versus M were also observed in soil enzyme activities and gene copy numbers of ammonia-oxidizing bacteria and denitrifiers. Our datasets suggest that BM interacted strongly with soil texture to modulate the pore scale-based diffusion of oxygen, thereby creating divergence in the aeration status among soils. Sequentially, soil phenol oxidase activity was greater in BM than in M under more aerobic conditions but no difference between BM and M in oxygen-limited soils. The balance between oxygen depletion due to microbial respiration of organic amendments and oxygen diffusion through soil/biochar pores also shaped the activities of nitrifying and denitrifying prokaryotes differently between coarse- and fine-textured soils. This logic model well-explained the magnitude of change in soil-dependent CO2 and N2O emissions from organic amendments. The knowledge gained in this work will likely have profound practical ramifications for optimizing BM efficacy in mitigating the GHGs emission.