Marine sediments are a natural laboratory for understanding how environmental factors shape life and geochemical processes over geologic time. A systematic approach to studying this enormous habitat on a large scale has been confounded by the difficulty of accessing marine sediments and the challenges associated with cultivating their microbial inhabitants. Therefore, the biodiversity and function of the marine subsurface biosphere, and the biogeochemical processes that subseafloor life mediates, remain elusive. Here, we combine reaction transport and power modelling with genomic datasets to better understand and quantify (1) the burial and degradation of organic carbon in marine sediments, (2) the energy flux that sustains subseafloor life, and (3) the links between energy and the structure and function of deep biosphere microorganisms. Closing the gap between biogeochemical and bio-energetic modelling and microbial ecology will ultimately reveal the boundaries of the deep biosphere, the rate at which it is active, which reactions are used to gain energy, and how it impacts Earth’s biogeochemical cycles.