Time-dependent density functional theory (TD-DFT) calculations were performed to obtain vertical excitation energies from the ground state to different low-lying singlet excited states of the protonated alpha-84 phycocyanobilin chromophore (alpha-84 PCBH+). It clearly emerges that three gradient-corrected approximation functionals (B3LYP, PBE0, and PBEPBE) show a similar description, confirming the proposed valence assignment of the strongest UV-vis absorption band at 618 nm. Moreover, our results show that there are not appreciable differences, in terms of excitation wavelength of the main peak, between the alpha-84 PCBH+ chromophore and a model system in which the two propionic chains have not been taken into account. Finally, with the precise aim of investigating the effects of alpha-84 PCBH+ conformational fluctuations on its electronic properties, vertical excitation energies obtained for the potential energy local minimum structure were also refined using a recently proposed TD-DFT/principal component analysis/Car-Parrinello molecular dynamics computational approach. Interestingly, and in line with previous results on another photosensitive complex, this study essentially suggests that interaction with the surrounding environment (protein matrix plus solvent molecules) coupled with the large amplitude fluctuation of the whole C-Phycocyanin (C-PC) pigment protein can affect the electronic properties of the alpha-84 PCB chromophore and therefore its biological activity.