Self‐assembly synthesis of mixed‐ligand (silsesquioxane/acetate) complex allows to isolate record high nuclear copper(II) Cu13‐cage (1). In the presence of two additional sodium ions, a unique molecular architecture, with triple combination of ligands (cyclic and acyclic silsesquioxanes as well as acetates), has been formed. The structure was established by single‐crystal X‐ray diffraction based on the use of synchrotron radiation. Complex 1 was evaluated as precatalyst in the Baeyer‐Villiger oxidation of cyclohexanone towards ε‐caprolactone, employing hydrogen peroxide, tert‐butyl hydroperoxide (TBHP) or m‐chloroperoxybenzoic acid (mCPBA) as oxidants, in an aqueous acidic acetonitrile medium. The direct formation of the lactone from cyclohexane via a tandem peroxidative oxidation/Baeyer‐Villiger oxidation was also studied. For both substrates, the best results (ε‐caprolactone yields up to 100% or 26%, from cyclohexanone or cyclohexane, respectively) were achieved with mCPBA under considerably mild conditions, i.e., conventional heating at 50 °C for 4 h or microwave (MW) irradiation at 80 °C for only 30 minutes.