Cryptochromes are essential flavoproteins for circadian rhythms and avian magnetoreception. Flavin adenine dinucleotide (FAD)a chromophore within cryptochromes, absorbs blue light, initiating electron transfer processes that lead to a biological signaling cascade. A key step in this cascade is the formation of the FAD semiquinone radical (FADH^•), characterized through a specific red-light absorption. The absorption spectra of FADH^• in cryptochromes are, however, significantly different from those recorded for the cofactor in solution, primarily due to protein-induced shifts in the absorption peaks. This study employs a multiscale approach, combining molecular dynamics (MD) simulations with quantum mechanical/molecular mechanical (QM/MM) methodologies, to investigate the influence of protein dynamics on embedded FADH^• absorption. We emphasize the role of the protein's polarizable environment in the shaping of the absorption spectrum crucial for accurate spectral predictions in cryptochromes. Our findings provide valuable insights into the absorption process advancing our understanding of cryptochrome functioning.