The photo-excited triplet state of Zn-protoporphyrin IX located in the heme pocket of human neuroglobin has been investigated by time-resolved EPR coupled to magnetophotoselection. The triplet state in the protein matrix has been compared with the model complex in organic glass, considering both non-coordinating and coordinating solvent mixtures. The protein matrix plays an important role in stabilizing the coordination of the embedded chromophore, resulting in a more homogeneous environment relative to that of the chromophore in a glassy solvent, even in the presence of an axial nitrogenous ligand like pyridine. The EPR spectral parameters point out a slow Jahn–Teller interconversion between slightly different triplet states, both in organic solvent and in the protein matrix. The EPR-magnetophotoselection allows us to propose a reinterpretation of the assignment of the Q bands in the electronic absorption spectrum.