In this paper, we have reported the influence of annealing treatment on structural, optical, electrical, and thermoelectric properties of MBE-grown ZnO on Si substrate. After growth, a set of as grown ZnO was annealed in oxygen environment at 500–800°C and another set was annealed in different environments (vacuum, oxygen, zinc, and vacuum + zinc) at 600°C for one hour in a programmable furnace. X-ray diffraction (XRD) results demonstrated that all annealed samples exhibited a major diffraction peak related to (002) plane. The full width at half maximum (FWHM) of this plane decreased and crystalline size increased for oxygen annealed sample and it increased when samples were annealed in zinc, vacuum, and successively annealed in vacuum and zinc. Further, photoluminescence spectrum revealed that the intensity of band edge emission increased and defect emission decreased as annealing temperature (oxygen environment) increased while it decreased for rest of annealing ambient. It is suspected that annealing in oxygen environment causes compensation of the oxygen vacancies by the incoming oxygen flux, while annealing in zinc and vacuum generates more oxygen vacancies. Hall and Seebeck measurements are also consistent with these arguments.