The use of supplementary cementitious materials to replace clinker is one of the most powerful levers to cut down the carbon footprint of cementitious materials. This has led to an increased interest in research on calcined clay limestone cement (CCLC) over the last years. In this study, we first demonstrate the effect of iron secondary phases on the performance of calcined clays in CCLC then we focus on the interaction of iron secondary phases with kaolinite in kaolinitic clays. The results indicate that iron phases affect the physiochemical properties of calcined clays and this is shown by the high specific surface area. Further analysis shows that the iron is likely spread through the kaolinite structure which evidences the likelihood of substitution of Al3+ by iron. This reduces the crystallinity of kaolinite as supported by XRD and FTIR analysis. It is possible that the structural disturbance gives rise to more active sites that increase solubility. These findings help us to better understand how iron interacts with kaolinite in calcined clays and how that impacts performance.