The dioxomolybdenum(VI) complexes [MoO2Cl2(PzPy)] (1) and [MoO2(OSiPh3)2(PzPy)] (5) (PzPy = 2-[3(5)-pyrazolyl]pyridine) were synthesized and characterized by vibrational spectroscopy, with assignments being supported by DFT calculations. Complex 5 was additionally characterized by single crystal X-ray diffraction. Recrystallization of 1 under different conditions originated crystal structures containing either the mononuclear [MoO2Cl2(PzPy)] complex co-crystallized with 2-[3(5)-pyrazolyl]pyridinium chloride, binuclear [Mo2O4(μ2-O)Cl2(PzPy)2] complexes, or the oxodiperoxomolybdenum(VI) complex [MoO(O2)2Cl(PzPyH)], in which a 2-[3(5)-pyrazolyl]pyridinium cation weakly interacts with the MoVI center via a pyrazolyl N-atom. The crystal packing in the different structures is mediated by a variety of supramolecular interactions: hydrogen bonding involving the pyridinium and/or pyrazolyl N−H groups, weak CH···O and CH···π contacts, and strong π−π stacking. Complexes 1 and 5 are moderately active catalysts for the epoxidation of cis-cyclooctene at 55 °C using tert-butylhydroperoxide as oxidant, giving 1,2-epoxycyclooctane as the only reaction product. Insoluble materials were recovered at the end of the first catalytic runs and characterized by IR spectroscopy, elemental analysis, scanning electron microscopy (SEM)-energy dispersive spectroscopy (EDS), and powder X-ray diffraction. For complex 5 the loss of the triphenylsiloxy ligands during the catalytic run resulted in the formation of a tetranuclear complex, [Mo4O8(μ2-O)4(PzPy)4]. The recovered solids could be used as efficient heterogeneous catalysts for the epoxidation of cyclooctene, showing no loss of catalytic performance between successive catalytic runs.