Previous studies have shown that microorganisms thrive in oligotrophic fracture systems, and metabolisms include consumption and production of methane. In the Laxemar, Götemar, and Forsmark areas of Sweden, ancient microbial activity has previously been demonstrated by large δ13CVPDB variability of carbonate vein infillings within granitic host rocks. Here, we apply carbonate clumped isotope thermometry to reconstruct the temperature of precipitation of the carbonate within these veins. The carbonate clumped isotope temperatures indicate that mineralization took place between 46°C and 108°C, in line with previously published fluid inclusion data (<50°C to 113°C). The new carbonate clumped isotope data more accurately narrows temperatures at the lower end of this range as fluid inclusions are not easily applicable below 80°C, a temperature regime of high importance for paleobiological reconstructions. Our results demonstrate that large volumes of biogenic carbonate cement were formed from low-temperature microbial processes in low-salinity water, succeeding calcite of deep brine origin. The known burial and thermal history of the region combined with our carbonate clumped isotope data place the microbial activity at the end of the Variscan orogeny and later events (e.g., Jurassic). Thus, carbonate clumped isotope thermometry reduces uncertainties in deep biosphere studies by providing more accurate temperature constraints in the low-temperature regime, the biogenic processes, and the origin of the diagenetic fluids.