The cements industry is increasingly under pressure to reduce carbon emissions while maintaining performance standards. Limestone calcined clay cement (LC3) presents a promising low-carbon alternative; however, its performance depends significantly on the type and reactivity of clay used. This study investigates the effect of three common low-grade clay minerals—kaolinite, montmorillonite, and illite—on the behavior of LC3 blends. The clays were thermally activated and characterized using X-ray diffraction (XRD), thermogravimetric analysis (TGA), X-ray fluorescence spectroscopy (XRF), and Blaine air permeability testing to evaluate their mineralogical composition, thermal behavior, chemical content, and fineness. Pozzolanic reactivity was assessed using the modified Chapelle test. Microstructural development was examined through scanning electron microscopy (SEM) of the hydrated specimens at 28 days. The results confirmed a strong correlation between clay reactivity and hydration performance. Kaolinite showed the highest reactivity and fineness, contributing to a dense microstructure with reduced portlandite and enhanced formation of calcium silicate hydrate. Montmorillonite demonstrated comparable strength and favorable hydration characteristics, while illite, though less reactive initially, showed acceptable long-term behavior. Although kaolinite delivered the best overall performance, its limited availability and higher cost suggest that montmorillonite and illite represent viable and cost-effective alternatives, particularly in regions where kaolinite is scarce. This study highlights the suitability of regionally available, low-grade clays for use in LC3 systems, supporting sustainable and economically viable cement production.