Quantum dots (QDs) are studied intensively nowadays as fluorescent probes for biomedical applications due to their high emission quantum yield, excellent resistance to photo-bleaching, photo-stability and large Stokes shift, when contrasted with commonly utilized organic fluorescent dyes. This study introduces a protein engineering approach to incorporate metal coordination sites for the sustainable synthesis and stabilization of biocompatible CdS QDs in proteins. The resulting protein-stabilized CdS QDs (Prot-QDs), generated by a green aqueous route at 37 ºC, are highly photo-luminescent and photo-stable, have a long shelf-life and high stability under physiological conditions. The Prot-QDs showed effective internalization and high fluorescence in cells, even at low doses, and biocompatibility. This work focuses on CdS QDs, since this composition has been extensively studied, however this approach could be easily translated to QDs with other metal composition. Here, protein design emerges as promising approach to generate protein-nanomaterial hybrids as broadly applicable tools in different applications such as light-emitting devices, metal ion detection, and biomedical applications.