In this contribution, the entangled two-photon absorption (ETPA) process on naturally occurring flavoproteins was studied. Low temperature responsive protein (LOT6P) and b-type dihydroorotate dehydrogenase (DHOD B), which possess flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) chromophores embedded in the protein environment, were investigated. The ETPA cross-section was measured, and we found that it increases when going from an aqueous solution of the free flavin chromophore to the chromophore embedded in the protein. This enhancement is particularly evident when entangled photons are used as excitation light compared to classical light. Our results prove the potential of ETPA as a sensing technique for fluorescent proteins even for those whose classical TPA cross-section is small compared to well-known fluorescent proteins.