A method for temporally and spatially aligning a laser-based x-ray source and maintaining alignment is disclosed. A pump laser beam, which interacts with a plasma source to create an electron beam, is aligned with the electron beam. A scattering laser beam is overlapped with the pump laser beam at an intersection point. The pump laser beam and scattering laser beam alignments are monitored and adjusted to maintain optimal alignment during operation of the laser-based x-ray source.