Carbonate minerals of the dolomite-ankerite and magnesite-siderite series are often found in sedimentary basins associated with economically viable ore deposits and as alteration product of Ca-Mg-Fe-silicates in igneous and metamorphic rocks. Analysis of oxygen and carbon isotopes in such carbonates gives important information, among others, on their evolution and spatial distribution during sediment burial and diagenesis, crystallization temperature during sedimentation, diagenesis and hydrothermal alteration, fluid and carbon sources, mechanisms of CO2 sequestration (e.g., (Śliwiński et al., 2016, 2018 and references therein). Because of their common chemical zoning at the microscale, in-situ techniques such as Secondary Ion Mass Spectrometry (SIMS) are fundamental to unravel intragrain and intergrain isotopic heterogeneities at scales < 50 µm. Due to instrumental artifacts, SIMS analyses need to be calibrated with matrix-matched reference materials to be accurate. This dataset describes a newly compiled set of Ca-Mg-Fe carbonates that were characterized for their mineralogical (XRD), major and minor element chemical composition (EPMA), oxygen and carbon isotopic composition by acid digestion gas-source isotope ratio mass spectrometry (GS-IRMS), and oxygen and carbon isotopic homogeneity at the microscale (SIMS). Three dolomites and one ankerite with Fe# (molar Fe/(Fe+Mg)) ranging from 0.0004 to 0.3429, one magnesite (Fe# = 0.0099) and one siderite (Fe# = 0.6152) are now available for the global SIMS community.