The microscopic protonation mechanism, at an inframolecular level, of norbadione A, a pigment extracted from mushrooms and known to complex cesium cations, was determined by using 1H NMR titrations and the cluster expansion method. This study revealed a pH dependent Z to E isomer switch that occurs in both pulvinic moieties. As a consequence, norbadione A can exist in solution in four stereomeric forms (E−E, E−Z, Z−E, and Z−Z), which can be of interest in the development of molecular-level devices. In the presence of 0.15 M NaCl, the calculated microconstants showed an unusual apparent cooperativity between the enol groups, which results from the release of the sodium cations upon protonation of norbadione A.