Fluorescent proteins (FPs), featuring the same chromophore but different chromophore-protein interactions, display remarkable spectral variations even when the same chromophore protonation state, i.e. the anionic state, is involved. We examine the mechanisms behind this tuning by means of structural analysis, molecular dynamics simulations, and vertical excitation energy calculations using QM/MM Time-Dependent Density Functional Theory (TD-DFT), CASPT2/CASSCF, and SAC-CI. The proteins under investigation include the structurally similar, though spectrally distinct, Dronpa and mTFP0.7, with absorption peaks at 453 and 503 nm, respectively. We extend our analysis to two Green Fluorescent Protein variants, GFP-S65T (absorption peak at 484 nm), for comparison with previous computational studies, and GFP-S65G/V68L/S72A/T203Y, a yellow fluorescent protein (514 nm), in order to include one of the most red-shifted FPs containing a GFP-like chromophore. We compare different choices of the QM system, and we discuss how molecular dynamics simulations affect the calculation of excitation energies, with respect to X-ray structures. We are able to partially reproduce the spectral tuning of the FPs and correlate it to the chromophore bond-length variations, as determined by specific interactions with the chromophore environment.