A critical assumption underlying in situ transmission electron microscopy studies is that the electron beam (e-beam) exposure does not fundamentally alter the intrinsic deformation behavior of the materials being probed. Here, we show that e-beam exposure causes increased dislocation activation and marked stress relaxation in aluminum and gold films spanning a range of thicknesses (80–400 nanometers) and grain sizes (50–220 nanometers). Furthermore, the e-beam induces anomalous sample necking, which unusually depends more on the e-beam diameter than intensity. Notably, the stress relaxation in both aluminum and gold occurs at beam energies well below their damage thresholds. More remarkably, the stress relaxation and/or sample necking is significantly more pronounced at lower accelerating voltages (120 kV versus 200 kV) in both the metals. These observations in aluminum and gold, two metals with highly dissimilar atomic weights and properties, indicate that e-beam exposure can cause anomalous behavior in a broad spectrum of nanostructured materials, and simultaneously suggest a strategy to minimize such artifacts.