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Abstract The geochemistry of tropical coral skeletons is widely used in paleoclimate reconstructions. However, sub‐aerially exposed corals may be affected by diagenesis, altering the aragonite skeleton through partial dissolution, or infilling of secondary minerals like calcite. We analyzed the impact of intra‐skeletal calcite on the geochemistry (δ¹⁸O, Sr/Ca, Mg/Ca, Li/Mg, Li/Ca, U/Ca, B/Ca, Ba/Ca, and Mn/Ca) of a sub‐aerially exposedPoritessp. coral. Each micro‐milled coral sample was split into two aliquots for geochemistry and X‐ray diffraction (XRD) analysis to quantify the direct impact of calcite on geochemistry. We modified the sample loading technique for XRD to detect low calcite levels (1%–2%; total uncertainty = 0.33%, 2σ) in small samples (∼7.5 mg). Calcite content ranged from 0% to 12.5%, with higher percentages coinciding with larger geochemical offsets. Sr/Ca, Li/Mg, Li/Ca, and δ¹⁸O‐derived sea‐surface temperature (SST) anomalies per 1% calcite were +0.43°C, +0.24°C, +0.11°C, and +0.008°C, respectively. A 3.6% calcite produces a Sr/Ca‐SST signal commensurate with local SST seasonality (∼1.5°C), which we propose as the cut‐off level for screening calcite diagenesis in paleo‐temperature reconstructions. Inclusion of intra‐skeletal calcite decreases B/Ca, Ba/Ca, and U/Ca values, and increases Mg/Ca values, and can therefore impact reconstructions of paleoclimate and the carbonate chemistry of the semi‐isolated calcifying fluid in corals. This study emphasizes the importance of quantifying fine‐scale calcite diagenesis to identify coral preservation levels and assure robust paleoclimate reconstructions.