The Mayans’ skill in crafting highly durable lime-based mortars from natural in-situ materials highlights the sophistication of their engineering. Characterization of such mortars can provide valuable insights into the phases that contribute to long-term physicochemical performance. This study presents Mayan mortar’s preliminary mineralogical characterization data collected from the Muyil pyramid (built around 300 B.C.) in Quintana Roo state of Mexico. Specifically, X-Ray Diffraction (XRD), and Thermogravimetric analysis (TGA) of the mortar indicate that mortar primarily comprises lime and calcareous soil. The strength gain is attributed mainly to the binding of soil particles from calcium carbonate precipitation. Representative modern mortar samples cast with lime and in-situ soil sourced from the Muyil pyramids indicate that the calcium carbonate polymorphs present in the soil played a critical role in the kinetics of carbonation. The high amounts of Aragonite and calcite in the in situ soil significantly enhance the carbonation kinetics and contribute to the strength improvement. Preliminary results from mineralogical characterization indicate that Aragonite and calcite act as nucleation sites, facilitating the improved kinetics of lime carbonation.