Noble metal quantum clusters (NMQCs) are considered to be the bridge between atoms and nanoparticles. They have dimensions comparable to the Fermi wavelength of electrons and have discrete energy levels due to quantum confinement which makes many of them luminescent in the visible region. NMQCs have been synthesized in the solution phase with various ligands, ranging from phosphines over four decades ago, to proteins, in the recent past. Brightly luminescent NMQCs embedded in proteins (NMQCs@proteins) make functional and smart hybrid materials, since proteins are functional soft biological nanomachines. The transdisciplinary and expansive nature of atomic cluster science is once again evident in this new entrant to the cluster family. In this chapter, structural, photo-physical aspects and applications of this new system are discussed in detail. Protein–metal ion adducts act as templates from which atomically precise gas phase clusters have been formed. Looking critically, several fundamental questions are yet to be answered in this emerging discipline, but we believe that the field will continue to evolve in terms of understanding and will be widely applied in several areas of sensing, catalysis, biology and medicine.