Abstract Present work reports on the electron irradiation induced modification in Au–Pd alloy based spherical shaped nanoparticles in scanning electron microscope (SEM). The Au–Pd alloy thin films were synthesized by DC sputtering of an Au–Pd alloy target and subsequent annealing at 800 °C. The composition and thickness of the as-deposited film was measured by Rutherford Backscattering Spectrometry (RBS). SEM confirmed the formation of spherical shaped Au–Pd alloy nanoparticles in annealed film. In-situ study on the transformation of Au–Pd alloy based spherical shaped nanoparticles to the Au@Au–Pd core-shell nanoparticles during electron irradiation in the SEM was performed. Structural characterizations were carried out by grazing incidence X-ray diffraction (GIXRD) and morphological changes were investigated qualitatively by grazing incidence small angle X-ray scattering (GISAXS) of the annealed film before and after electron irradiation. Theoretical calculations of electron energy loss indicate neither knock-on displacements nor temperature rise are responsible for structural transition observed in present case. It is suggested that electronic-excitations induced atomic displacements may cause spherical to core-shell phase transition.