A wafer-based charged particle accelerator includes a charged particle source and at least one RF charged particle accelerator wafer sub-assembly and a power supply coupled to the at least one RF charged particle accelerator wafer sub-assembly. The wafer-based charged particle accelerator may further include a beam current-sensor. The wafer-based charged particle accelerator may further include at least a second RF charged particle accelerator wafer sub-assembly and at least one ESQ charged particle focusing wafer. Fabrication methods are disclosed for RF charged particle accelerator wafer sub-assemblies, ESQ charged particle focusing wafers, and the wafer-based charged particle accelerator.