Limestone Calcined Clay Cements (LC3) are binders with complex phase development and microstructures. Although the hydration chemistry of these cements is widely researched, due to the clay mineralogy variability, more studies are needed to build full knowledge. This work is part of our ongoing research dealing with LC3 binders based on Spanish calcined clays. Three commercially available kaolinitic clays with different kaolinite contents (~83, ~74, and ~70 wt%) were selected, which were activated by calcination at 860ºC, and further milled down to Dv,50 values from 6 to 10 μm. LC3 binders were prepared with 52 wt% 42.5R Portland cement, 30 wt% calcined clay, 15 wt% limestone, and 3 wt% additional gypsum. Here, the phase assemblages, determined by Rietveld quantitative phase analysis and thermal studies, at 2, 7, 28, and 120 days for the three LC3 families (pastes) prepared with a water-to-binder ratio of 0.40 are reported. The results are compared with porosimetry data for the pastes and the mechanical strengths of the corresponding mortars. This work supports the fact that, at 2 and 7 days, the pozzolanic effect is related to the surface area of the clay and disorder of the calcined clay (metakaolin); however, at higher ages, 28 and 120 days, the metakaolin content is the key feature to justify the measured mechanical strengths.