In this work we report on the formation and stability under thermal annealing of Pd–Cu and Pd–Ag alloy nanoclusters obtained by sequential ion implantation in silica. The role of the annealing atmosphere on the alloy cluster formation and stability is investigated. A comparison is made with similar alloy-based systems obtained by sequential ion implantation in silica of Au–Ag or Au–Cu followed by annealing under similar conditions, in order to evidence the peculiar effect of the various metals in controlling the alloy evolution and/or decomposition.