Chloride binding is an important factor for chloride transport in cementitious materials, which can fix the chloride on the solid phase and decrease the free chloride content. As an alumina-rich supplementary cementitious material, calcined clay can be applied to improve the binding capacity of the system. While the contribution of calcined clay to chemical binding (through the formation of Friedel’s salt) is clear, its influence on physical binding (adsorption on hydration products) is still under debate. In this study, pure C3S instead of cement was used to assess the binding capacity on the presence of calcined clay. In addition, extra limestone was added to investigate the synergetic effect between calcined clay and limestone on binding capacity. Binding capacity was evaluated by an equilibrium method between free chloride in the solution and bound chloride in the solid phase. The evolution of the phase assemblage was analyzed using XRD-Rietveld, the pore structure, and the specific surface area were measured with the nitrogen adsorption method. It was observed that the systems with calcined clay present higher binding capacity than the reference. In addition, the binary system demonstrates similar bound chloride content compared to the ternary system. Characterization results were used to correlate the microstructural properties of cementitious materials to chloride binding capacity. Results showed that the calcined clay contributes to the chemical binding and, that there is no clear relation between specific surface area and physical binding in cementitious materials.