Metabolic activities of soil microbes are the primary drivers of biogeochemical processes controlling the terrestrial carbon cycle, nutrient availability to plants, contaminant remediation, and other ecosystem services. However, we have a limited understanding of how microbes and microbial metabolism are distributed throughout the three-dimensional complex of the soil, or how this impacts emergent properties like microbial diversity or biogeochemical fluxes. To improve our understanding of the constraints on microbial metabolic processes and their role in coupled carbon climate models, it is imperative to close this knowledge gap. I will discuss how microbially mediated physico-chemical protection mechanisms affect the accumulation and longevity of soil organic matter pools, and how the microbial communities responsible for these mechanisms vary over a landscape. Finally, I will discuss ongoing research to identify where microbial  metabolic process occur in the complex system of the soil pore network.