Cryoconite holes, which can cover 0.1–10% of the surface area of glaciers, are small, water-filled depressions (typically <1 m in diameter and usually <0.5 m deep) that form on the surface of glaciers when solar-heated inorganic and organic debris melts into the ice. Recent studies show that cryoconites are colonized by a diverse range of microorganisms, including viruses, bacteria and algae. Whether microbial communities on the surface of glaciers are actively influencing biogeochemical cycles or are just present in a dormant state has been a matter of debate for long time. Here, we report primary production and community respiration of cryoconite holes upon glaciers in Svalbard, Greenland and the European Alps. Microbial activity in cryoconite holes is high despite maximum temperatures seldom exceeding 0.1 °C. In situ primary production and respiration in cryoconites during the summer is often comparable with that found in soils in warmer and nutrient richer regions. Considering only glacier areas outside Antarctica and a conservative average cryoconite distribution on glacial surfaces, we found that on a global basis cryoconite holes have the potential to fix as much as 64 Gg of carbon per year (i.e. 98 Gg of photosynthesis minus 34 Gg of community respiration). Most lakes and rivers are generally considered as heterotrophic systems, but our results suggest that glaciers, which contain 75% of the freshwater of the planet, are largely autotrophic systems.