Cryptochromes are a class of light-absorbing proteins that have been shown to be a part of thecircadian rhythm of many animals but seem to play a central role for the magnetosensing of migratory birds. Following a documented difference in the sensitivity to an external magnetic field of cryptochrome 4a proteins from migratory and non-migratory birds, a detailed analysis of inter- and intra-protein energetics is called for. The present study relies on classical molecular dynamics simulations of cryptochrome 4a from five avian species to reveal if any of the cryptochromes feature peculiarities in their internal energetics. The five avian cryptochrome 4a proteins from pigeon, European robin, zebra finch, chicken, and Eurasian blackcap are found to be highly similar in respect of their intra-energetic behaviors, while some minor differences between the cryptochromes can be ascribed to the site of specific structural differences. Particular attention has been paid to account for the interaction of the protein with the solvent, and it has been revealed that the solvent could lead to significant stabilization of the chromophore flavin adenine dinucleotide inside of the cryptochrome 4a scaffold.