AbstractBoron geochemistry from biogenic carbonates offer valuable information about ocean pH and CO2 chemistry. However, application to geological carbonate deposits suffers from analytical difficulties in obtaining geochemical signals exclusively from the carbonate phase. Sequential leaching with reagents and acids has the potential to overcome such an issue. There is, however, little systematic investigation about the efficiency of sequential leaching in isolating carbonate‐associated boron from siliciclastic matrix. Here, we developed a sequential leaching protocol and applied it to methane‐derived‐authigenic‐carbonate samples. Using the leachate δ11B signatures, elemental composition, and mineral composition of residues, we show that the sequential leaching is able to improve the separation of boron from different phases. Buffered hydrogen peroxide removes organic matter and also some silicate phases resulting low δ11B values. Leaching with NH4Ac removes adsorbed boron though may also partially leach some carbonate phases. The first few leaching steps with diluted acetic acid dissolve carbonate phases. Depending on the sample type, these may also capture some remaining adsorbed boron from the preceding NH4Ac leaching. Once the adsorbed boron is completely removed, as indicated by the progressively higher δ11B values during the following acid leaching steps, representative carbonate composition can be derived. The accuracy of this protocol is demonstrated with leaching experiments using artificial deep sea coral carbonate and clay mixtures that give the representative carbonate‐associated δ11B within error of the pure coral value. Our results provide insights into characteristic signatures derived from silicates and organic matter that need to be considered in boron isotope analyses of impure marine carbonates.