In situ elemental analysis of carbonate matrices at the microscale is a rapidly developing and promising area of research with significant implications for fields including geology, environmental science, and biology. However, applications in these fields have been hampered by the lack of appropriate analytical reference materials and the ongoing need for improvements in analytical methods. This study used pure ooid sands from the modern Schooner Cays in the Bahamas as raw material due to their nearly consistent mineralogical compositions and uniform elemental distributions. A wet milling process was employed, and the Tyndall effect was used to isolate ultra-fine colloidal particles (most <1 μm). These particles underwent high-pressure compression, and the resulting pellets, namely OOID, were subsequently embedded in epoxy resin to ensure their long-term preservation and utility. Over a four-year study period, we confirmed that at least 28 elements remained homogeneously distributed within the reference material OOID. These results were achieved through rigorous relative standard deviation and Horwitz tests. The findings of this study underscored the crucial role of natural reference materials in ensuring quality control of in situ carbonate elemental analyses. Simultaneously, the study provided valuable new guidelines for preparing carbonate reference materials and improved the accuracy of in situ microanalytical methods for carbonate samples.