We report the synthesis of luminescent AuAg alloy quantum clusters (QCs) in bovine serum albumin (BSA), for the first time, with experimentally determined atomic composition. Mixing of the as-synthesized protein-protected Au and Ag clusters resulted in the formation of alloy AuAg clusters within the BSA. Mass spectrometric analysis of the product of a 1:1 molar ratio reaction mixture of AuQC@BSA and AgQC@BSA suggested that the alloy clusters could be Au38-xAgx@BSA. Further analyses by standard techniques revealed that the alloy cluster core of ∼1.2 nm diameter is composed of nearly zero valent Au and Ag atoms that exhibit distinctly different steady state and time resolved excited state luminescence profiles compared to the parent clusters. Tuning of the alloy composition was achieved by varying the molar ratio of the parent species in the reaction mixture and compositional changes were observed by mass spectrometry. In another approach, mixing of Au3+ ions with the as-synthesized AgQC@BSA also resulted in the formation of alloy clusters through galvanic exchange reactions. We believe that alloy clusters with the combined properties of the constituents in versatile protein templates would have potential applications in the future. The work presents interesting aspects of the reactivity of the protein-protected clusters. © 2012 The Royal Society of Chemistry.