Difference patterns of 13C NMR chemicals shifts for the protonation of a free model compound in organic solution, as reported in the literature (M. Stanek, K. Grubmayr  Chem. Eur. J.4, 1653–1659), were compared with changes in the protonation state occurring during holophytochrome assembly from phycocyanobilin (PCB) and the apoprotein. Both processes induce identical changes in the NMR signals, indicating that the assembly process is linked to protonation of the chromophore, yielding a cationic cofactor in a heterogeneous, quasi-liquid protein environment. The identity of both difference patterns implies that the protonation of a model compound in solution causes a partial stretching of the geometry of the macrocycle as found in the protein. In fact, the similarity of the difference pattern within the bilin family for identical chemical transformations represents a basis for future theoretical analysis. On the other hand, the change of the 13C NMR chemical shift pattern upon the Pr → Pfr photoisomerization is very different to that of the free model compound upon ZZZ → ZZE photoisomerization. Hence, the character of the double-bond isomerization in phytochrome is essentially different from that of a classical photoinduced double-bond isomerization, emphasizing the role of the protein environment in the modulation of this light-induced process.