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Carbonate materials – limestone and lime stuccos – were widely used in ancient Maya construction. Deterioration of these materials presents a major problem for the conservation of Maya architectural heritage. However, the mechanisms of deterioration and their interaction with the diverse inner structures of these materials are still insufficiently understood. We performed micromorphological and mineralogical research of the limestone alteration in the buildings of Rio Bec and stuccos in Dzibanche, two Late Classic Maya sites in the southern Yucatan peninsula. Dissolution and recrystallization of calcite were found to be universal and the most important weathering process in both materials. Dissolution is selective, affecting mostly micrite. Larger crystals, especially rhombohedral calcitic pseudomorphs developed after dolomite, are more stable. Selective dissolution of micritic cement of limestones and stuccoes enhances physical breakdown by producing numerous pores and loosening bounds between coarser inclusions. This process clearly controls the deterioration grade of different limestones: those with more intensive fragmentation and powdering have higher contents of micrite. Secondary carbonates are represented mostly by acicular calcite filling fissures and forming coatings on the outer surface. Clear spatial relation to fungi and roots and their similarity to well-known soil neoformations indicate biogenic origin of these neoformations. In most cases, they contribute to macroscopic powdering being loose. However, in the cracks of some limestones they form dense infillings, which could plug the fractures and prevent further advance of weathering to the core of the stone. Neoformed sulfates and iron oxides are fewer, but also participate in the deterioration.