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During the Noachian, Mars' crust may have provided a favorable environment for microbial life. The porous brine-saturated regolith would have created a physical space sheltered from UV and cosmic radiations and provided a solvent, while the below-ground temperature and diffusion of a dense reduced atmosphere may have supported simple microbial organisms that consume H2 and CO2 as energy and carbon sources and produce methane as a waste. On Earth, hydrogenotrophic methanogenesis was among the earliest metabolisms but its viability on early Mars has never been quantitatively evaluated. Here we present a probabilistic assessment of Mars' Noachian habitability to H2-based methanogens, and quantify their biological feedback on Mars' atmosphere and climate. We find that subsurface habitability was very likely, and limited mainly by the extent of surface ice coverage. Biomass productivity could have been as high as in early Earth's ocean. However, the predicted atmospheric composition shift caused by methanogenesis would have triggered a global cooling event, ending potential early warm conditions, compromising surface habitability and forcing the biosphere deep into the Martian crust. Spatial projections of our predictions point to lowland sites at low-to-medium latitudes as good candidates to uncover traces of this early life at or near the surface.