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Microorganisms inhabiting terrestrial endolithic habitats are widespread in polar environments including the Antarctic Dry Valleys and the Canadian high Arctic. Their ability to survive in these harsh environments is a result of their finding protection from extremes in temperature, aridity, radiation and winds by colonizing nutrient-rich subsurface habitats that provide more amenable conditions for growth, often developing as vertically stratified communities that include fungi, algae, cyanobacteria and heterotrophic bacteria. Despite finding some refuge from climatic extremes, endolithic microorganisms commonly produce extracellular polysaccharides to avoid desiccation and minimize the damaging effects of freeze-thaw cycles. These microorganisms are geochemically reactive with their endolithic surroundings, observed as heterogeneous concentrations and distributions of metals resulting from mineral dissolution and precipitation reactions as well as element and nutrient release and cycling. Novel microscopy techniques such as SEM-BSE reveal much information about the physiological state of these microorganisms in situ, and show how under specific conditions, microbe-mineral interactions produce unique biosignatures of interest to studies in astrobiology. Their ability to change in situ pH conditions shows that can be directly involved in weathering of endolithic habitats, but the ecology of a given endolithic microbial community can have varying effects on rates of rock weathering. These differences in weathering rates may be an important control on microbial species diversity in polar desert endolithic habitats.