A high-power microwave (HPM) vacuum tube source and method of precise coaxial alignment of the field emission (FE) cathode, cylindrical RF generating tube and magnet field includes positioning a low-power thermionic emission (TE) cathode inside the FE cathode in a “cathode-in-cathode” arrangement. With the HPM source under vacuum and the FE cathode deactivated, the TE cathode emits a surrogate electron beam through the generating tube. Measurement circuits measure the surrogate electron beam's position with respect to a longitudinal axis fore and aft of the generating tube. The measurements circuits may, for example, be a repositionable fluorescent target or electric field sensors embedded in the cylindrical RF generating tube. The coaxial alignment of the primary cathode, cylindrical RE generating tube and magnet is adjusted until the position of the surrogate electron beam satisfies a coaxial alignment tolerance.