Association of indigo and lapachol dyes to aluminosilicate clays yields polyfunctional organic–inorganic hybrid materials forming Maya Blue-like systems. Upon partial removing of clay's zeolitic water by moderate thermal treatment, abundant isomerization, cyclicization and oxidation reactions occur defining a ‘Maya chemistry’ whose complexity could explain the versatile use of such materials in the pre-Columbian cultures and permits the preparation of polyfunctional materials potentially usable for therapeutic and catalytic purposes.