Maya Blue is a puzzling pigment found in objects produced by the ancient Maya civilization. It is a combination of indigo and palygorskite, and it is well-known for the high chemical and photochemical stability of the dye promoted by the clay confined environment. This pigment has survived over 1500 years, and it was first thought to be purely inorganic. The reasons for such stability have been investigated over the past years, and it may involve hydrogen bonds, complexation, and oxidation to dehydroindigo. However, these theories are not completely understood, and more evidence about indigo/palygorskite interactions must be obtained. In this study indigo and a Maya Blue simulant pigment were, for the first time, studied by transient absorption (TA) and time-resolved infrared (TRIR) spectroscopy. From such analysis it was possible to investigate the electronic excited states of indigo and the photochemistry behavior of the dye when interacting with the palygorskite. Concerning the TRIR measurements, the shifts of the C O and N−H vibrations indicate that hydrogen bonds are formed involving the dye and the coordinated water molecules present in the clay. Furthermore, a red shift is observed in the absorption of electronic ground state (50 nm) and also in the electronic excited state (27 nm) of Maya Blue simulant, suggesting that the excited states are stabilized by the clay. Indigo in DMSO solution presents a lifetime of ca. 120 ps while in the clay it becomes much shorter, ca. 3 ps. The shorter lifetime and also the red shift observed in the TA results suggest a stabilization of the first electronic excited state, which promotes a more efficient energy relaxation through conical intersection and, as a consequence, a faster excited state decay. Such factors can be important for the Maya Blue photostability, as they are also believed to be responsible for the high photostability of DNA and melanin.