Rationale Understanding changes in Earth's oceans and climate requires the reliable application of paleo‐proxies. However, inconsistencies between individual δ 18 O records within biogenic specimens commonly have significant impacts on environmental reconstructions. This study addresses the stable isotope variability associated with sample milling from aragonitic organisms commonly used for paleoclimate studies. Methods Aragonite samples were hand‐ground and milled from sclerosponge, coral, and mollusc specimens using a computerized micromill. An X‐ray diffractometer was used to analyze sample mineralogy prior to measurement of δ 18 O and δ 13 C values via isotope ratio mass spectrometry of CO 2 gases provided from the samples by a Kiel III device. Possible influences on the Sr/Ca ratios were assessed on a sclerosponge through paired elemental analysis by inductively coupled plasma optical emission spectrometry. Results Analyses revealed up to 36% inversion to calcite in milled samples that correlated with a decrease in the δ 18 O value of 0.02 ‰ per 1% inversion. Replicate sclerosponge transects yielded similar trends in δ 13 C values and Sr/Ca ratios, although the δ 18 O values showed irregular variations consistent with those measured for the inversion of individual organisms during milling. Conclusions While the δ 13 C values and Sr/Ca ratios of milled samples were largely consistent, the δ 18 O values co‐varied with the inversion of aragonite to calcite suggesting significant implications for the resulting temperature and salinity reconstructions from aragonitic archives. The effect appears to be density‐driven and, given that the skeletal density tends to vary seasonally in organisms such as corals, would subsequently mask temperature‐induced changes in skeletal δ 18 O values. Copyright © 2015 John Wiley & Sons, Ltd.