Maya blue is an ancient nanostructured pigment synthetized by assembling indigo, a natural dye, with palygorskite, a microfibrous clay mineral. The novelty of our approach is to mimic “pre-Columbian nanotechnology” and to functionalize geopolymers with a sepiolite-based hybrid organic–inorganic nanocomposite inspired from the Maya blue. It is acid- and UV-resistant, as confirmed by the stability of Maya mural paintings over time. We synthesized analogous pigments, using methylene blue (MB) and methyl red (MR) as organic dyes and sepiolite as fibrous clay mineral. We used an aqueous and a solid-state method, both leading to encapsulation of dye monomers into the clay micropores, as confirmed by UV-vis spectroscopy. This nanostructured pigment was then included into a geopolymer matrix at room temperature. The stability of the new material to UV and acid was tested. It was confirmed that it is the prior encapsulation of the dye into sepiolite that leads to the stability of the pigment in the geopolymer matrix. This first study opens the way to numerous possibilities for functionalizing inorganic binder materials with organic elements that would be otherwise sensitive to thermal treatment in conventional ceramic processing.