The goal of this study is the preparation of new heterogeneous catalysts to be used in the oxidation of organic molecules under mild conditions. The metals in zeolite (M–Y) were prepared by the ion exchange method. The in situ encapsulation of selected transition metal complexes as a guest, namely cobalt(II), nickel(II), copper(II), and zinc(II), with 1-(2-pyridylazo)-2-naphthol (PAN) ligand in supercages of Y zeolite (host) was accomplished by the flexible ligand method. The coordination geometry of neat and Y-encapsulated metal complexes has been determined by molecular simulations. The resulting catalysts were fully characterized by different techniques (FTIR, SEM, and chemical analysis), and the results indicated that complexes were encapsulated in supercages of Y zeolite. Catalytic studies were performed in liquid phase for cyclohexene and cyclohexanol oxidations, by using tert-butylhydroperoxide as the oxidizing agent at 40 and 60°C, respectively. All prepared catalysts exhibited catalytic activity for the oxidation reactions.