The Kupferschiefer district in Central Europe contains some of the world's highest-grade sediment-hosted stratiform Cu (SSC) deposits. In the Saale subbasin (eastern Germany), high-grade sulfides formed via replacement of calcite cement in the continental sandstones of the uppermost Rotliegend (S1), the overlying organic-rich marine mudstones of the Kupferschiefer (T1) and the Zechstein Limestone (Ca1) units. The spatial distribution of the calcite cement, therefore, had a fundamental role to play in the Cu mineralizing system. In this study, we investigate the origin of the calcite cement (and crosscutting calcite veins) using detailed petrography (cathodoluminescence, CL; scanning electron microscopy, SEM), major element chemistry (electron probe microanalyzer, EPMA), and secondary ion mass spectrometry (SIMS) microanalyses of δ13C and δ18O values in drill core samples (n = 47) from the Saale subbasin. The calcite cement in the S1, T1 and Ca1 has a similar CL response and major element chemistry, suggestive of a common origin. Overlapping δ13C and δ18O values in calcite cement in samples from the S1 and T1 in the Sangerhausen and Wallendorf drill cores also suggest that the calcite cement was derived from fluids of similar composition. The low δ13C values of calcite cement in samples from the S1 (−13‰ to 4.3‰, VPDB) and T1 (−10‰ to 0.7‰) indicates carbonate alkalinity was sourced mainly from seawater-derived fluids and the oxidation of organic matter. The wide range of δ18O values in the calcite cement in the S1 (∼18‰ to 31‰, VSMOW) and T1 (∼ 22‰ to 31‰) samples suggest they are derived from pore fluids with a chemical composition influenced by early diagenetic alteration of detrital clasts, mainly dissolution of volcanic rock fragments, with minor contributions from the influx of meteoric waters and evaporated seawater. The negative δ13C values (down to −15‰) in calcite veins from the T1 and Ca1 indicate sources of carbonate alkalinity derived from organic matter degradation. Our data demonstrate that no isotopic hydrothermal alteration haloes can be inferred from the δ13C and δ18O values in calcite cement associated with the high-grade sulfide mineralization. The lack of systematic isotopic variability in the calcite cement likely indicates the mineralizing fluid flux or temperature was not sufficient to overprint the background sources of isotopic variability, which may help to explain the modest size of SSC deposits in this part of the Kupferschiefer district.