Soil structure and interactions between biotic and abiotic processes are increasingly recognized as important for explaining the large uncertainties in the outputs of macroscopic SOM decomposition models. We present a numerical analysis to assess the role of meso- and macropore topology on the biodegradation of a soluble carbon substrate in variably water saturated and pure diffusion conditions . Our analysis was built as a complete factorial design and used a new 3D pore-scale model, LBioS, that couples a diffusion Lattice-Boltzmann model and a compartmental biodegradation model. The scenarios combined contrasted modalities of four factors: meso- and macropore space geometry, water saturation, bacterial distribution and physiology. A global sensitivity analysis of these factors highlighted the role of physical factors in the biodegradation kinetics of our scenarios. Bacteria location explained 28% of the total variance in substrate concentration in all scenarios, while the interactions among location, saturation and geometry explained up to 51% of it.