This data publication is supplementary to a study on microbial weathering of Fe-bearing minerals in the deep biosphere of a semi-arid environment (Chile). The dataset contains mineralogical, geochemical, microbiological and thermodynamic data of an 87 m deep drill core profile located in the Chilean Coastal Cordillera (Santa Gracia (SG)). The drilling campaign was conducted in March-April 2019 as part of the German Science Foundation (DFG) priority research program SPP 1803 “EarthShape: Earth Surface Shaping by Biota”. The project focused on how microorganisms contribute to mineral weathering and thus shape Earth´s surface. Aim of the drilling campaign was to recover the continuous weathering profile from surface to weathering front and to pinpoint as well as disentangle weathering processes at depth. For this purpose, extractable Fe pools, water-extractable organic carbon and nitrate, energy yields of Fe redox reactions, in situ microbial Fe(III) reduction, microbial Fe(III) reduction extent in microcosms, as well as community compositions of in situ and microcosms derived 16S rRNA gene amplicon sequence variants (ASVs) were determined.