The kaolinite content is principally responsible for the durability performance of Limestone Calcined Clay Cement (LC3), which calls into question its global applicability. The clay supply has a significant impact on the LC3 system’s reduced carbon footprint advantage. The influence of kaolinite concentration from two separate clays (collected in East South-East Europe) on the durability performance of concrete was investigated in this study. The low-kaolinitic clay had 18% kaolinite, while the medium-kaolinitic clay contained around 41% kaolinite. The compressive strength, chloride intrusion, electrical conductivity, surface resistivity, and sorptivity index were measured on concrete after 28 days. Furthermore, the pore structure development of these mixtures was investigated in relation to the kaolinite content of the mixtures. The reactivity test was performed on clays to measure their reactivity levels within the cementitious system. The results show that kaolinite content has a moderate effect on compressive strength, but it has a considerable effect on other durability indices. When compared to the Portland cement mixture, the chloride migration and diffusion coefficients were reduced by 50% and 36%, respectively, in the combination with a medium kaolinite content (more than 40%). The low-kaolinitic clay, on the other hand, achieved 60% of the chloride penetration resistance of the medium-kaolinitic clay. Furthermore, low-kaolinitic clay has been demonstrated to be suitable for low-carbon concrete in moderate exposure conditions.