Electron irradiation during reflection high-energy electron diffraction is shown to affect the materials properties of ZnSe and GaN during growth by molecular beam epitaxy. The high-energy electrons produce an electron stimulated desorption effect during growth of ZnSe, which primarily affects adsorbed Se. Se desorption rates under electron irradiation are shown to be significantly larger than thermal desorption rates. Electron irradiation also decreases ZnSe growth rates under Zn-rich conditions. The decrease can be suppressed by either growth under Se-rich conditions or by using high index substrate orientations, in this case (211)B. Electron irradiation also influences growth rates for GaN grown by rf plasma-assisted molecular beam. Characterization using Raman and photoluminescence spectroscopy along with secondary ion mass spectrometry indicate electron irradiation can have a dramatic impact on point defect and impurity content of GaN.