In this paper, we present a study of various ZnO/SiO2-stacked thin film structures for flexible micro-energy harvesting devices. Two groups of micro-energy harvesting devices, SiO2/ZnO/SiO2 micro-energy generators (SZS-MGs) and ZnO/SiO2/ZnO micro-energy generators (ZSZ-MGs), were fabricated by stacking both SiO2 and ZnO thin films, and the resulting devices were characterized. With a particular interest in the fabrication of flexible devices, all the ZnO and SiO2 thin films were deposited on indium tin oxide (ITO)-coated polyethylene naphthalate (PEN) substrates using a radio frequency (RF) magnetron sputtering technique. The effects of the thickness and/or position of the SiO2 films on the device performance were investigated by observing the variations of output voltage in comparison with that of a control sample. As a result, compared to the ZnO single-layer device, all the ZSZ-MGs showed much better output voltages, while all the SZS-MG showed only slightly better output voltages. Among the ZSZ-MGs, the highest output voltages were obtained from the ZSZ-MGs where the SiO2 thin films were deposited using a deposition power of 150W. Overall, the device performance seems to depend significantly on the position as well as the thickness of the SiO2 thin films in the ZnO/SiO2-stacked multilayer structures, in addition to the processing conditions.