This study investigated the physicochemical effects of kaolinite (CK) and montmorillonite (CM) calcined clays on the sulfate balance, early hydration, and artificial pore solution of limestone calcined clay cement (LC3). The effects of fineness, clay dissolution, and ion-adsorption capacity were evaluated by isothermal calorimetry, compressive strength, ICP-OES, and zeta potential within 72 hours, respectively. Increasing the fineness of both calcined clays did not significantly affect the sulfate depletion kinetics or the compressive strength and the adsorption of Ca2+ ions onto the calcined clay’s surface is not the main factor responsible for differences in sulfate demand. The higher dissolution of ions Al in CK provided an intensified and accelerated formation of ettringite that competes for the available sulfate. We demonstrate that the chemical effects have a significant impact on the sulfate balance of LC3, revealing the lesser impact of alternative clays like montmorillonite compared to metakaolin which can minimize the problem of accelerated sulfate depletion of LC3 mixes with MK.