Semiconductor nanoparticles are deposited on a top surface of a first insulator layer of a substrate. A second insulator layer is deposited over the semiconductor nanoparticles and the first insulator layer. A semiconductor layer is then bonded to the second insulator layer to provide a semiconductor-on-insulator substrate, which includes a buried insulator layer including the first and second insulator layers and embedded semiconductor nanoparticles therein. Back gate electrodes are formed underneath the buried insulator layer, and shallow trench isolation structures are formed to isolate the back gate electrodes. Field effect transistors are formed in a memory device region and a logic device region employing same processing steps. The embedded nanoparticles can be employed as a charge storage element of non-volatile memory devices, in which charge carriers tunnel through the second insulator layer into or out of the semiconductor nanoparticles during writing and erasing.