Cave carbonate mineral deposits (speleothems) contain trace elements that are intensively investigated for their significance as palaeoclimate and environmental proxies. However, chlorine, which is abundant in marine and meteoric waters, has been overlooked as a potential palaeo-proxy, while cosmogenic 36Cl could, in principle, provide a solar irradiance proxy. Here, total Cl concentrations analysed from various speleothems were low (3–14 mg/kg), with variations linked to crystal fabrics. High-resolution synchrotron radiation micro X-ray fluorescence (μ-XRF) trace element mapping showed Cl often associated with Na, Si, and Al. We propose that speleothems incorporate Cl in two fractions: (1) water soluble (e.g., fluid inclusions) and (2) water insoluble and strongly bound (e.g., associated with detrital particulates). However, disparities indicated that alternate unidentified mechanisms for Cl incorporation were present, raising important questions regarding incorporation of many trace elements into speleothems. Our first measurements of 36Cl/Cl ratios in speleothems required large samples due to low Cl concentrations, limiting the potential of 36Cl as a solar irradiance proxy. Critically, our findings highlight a knowledge gap into how Cl and other trace elements are incorporated into speleothems, how the incorporation mechanisms and final elemental concentrations are related to speleothem fabrics, and the significance this may have for how trace elements in speleothems are interpreted as palaeoclimate proxies.