This study explores the effects of cation composition on mass bias (i.e., the matrix effect), which is a major component of instrumental mass fractionation (IMF) in the microanalyses of δ13C and δ18O by SIMS in carbonates of the magnesite–siderite solid‐solution series (MgCO3–FeCO3). A suite of twelve calibration reference materials (RMs) was developed and documented (calibrated range: Fe# = 0.002–0.997, where Fe# = molar Fe/[Mg + Fe]), along with empirical expressions for regressing calibration data (affording residuals < 0.5‰ relative to certified reference material NIST‐19). The calibration curves of both isotope systems are non‐linear and have, over a 2‐year period, fallen into one of two distinct but largely self‐consistent shape categories (data from ten measurement sessions), despite adherence to well‐established analytical protocols for carbonate δ13C and δ18O analyses at WiscSIMS (CAMECA IMS 1280). Mass bias was consistently most sensitive to changes in composition near the magnesite end‐member (Fe# 0–0.2), deviating by up to 4.5‰ (δ13C) and 14‰ (δ18O) with increasing Fe content. The cause of variability in calibration curve shapes is not well understood at present and demonstrates the importance of having available a sufficient number of well‐characterised RMs so that potential complexities of curvature can be adequately delineated and accounted for on a session‐by‐session basis.