Diatoms are one of the most abundant photosynthetic organisms on earth and contribute largely to the atmospheric oxygen production. They contain fucoxanthin and chlorophyll-a/c binding proteins (FCPs) as light-harvesting complexes with a remarkable adaptation to the fluctuating light on ocean surfaces. To understand the basis of the photosynthetic process in diatoms, the excitation energy funneling within FCPs needs to be probed. A state-of-the-art multiscale analysis within a quantum mechanics/molecular mechanics framework has been employed. To this end, the chlorophyll (Chl) excitation energies within the FCP complex from the diatom Phaeodactylum tricornutum have been determined. The Chl-c excitation energies were found to be significantly lower than those in organic solvents. This finding challenges the general belief that the excitation energy of Chl-c is higher than that of Chl-a in FCP proteins and reveals that Chl-c molecules are much more sensitive to electric fields within protein scaffolds than Chl-a pigments. A direct connection to experiment is obtained by analysis of the linear absorption spectrum of FCP.