Abstract Exit wavefunction reconstruction is important in transmission electron microscopy for structural studies. We describe electron Fourier ptychography and its application to phase reconstruction of both radiation-resistant and beam-sensitive materials. We demonstrate that the phase of the exit wave can be reconstructed to high resolution using a modified iterative phase retrieval algorithm from data collected in an alternative optical geometry. This method achieves a spatial resolution of 0.63 nm at a fluence of 4.5 × 10 2 e − /nm 2 , as validated on Cry11Aa protein crystals under cryogenic conditions. Notably, this method requires no instrumental modifications, is straightforward to implement, and can be seamlessly integrated with existing data collection software, providing a broadly accessible alternative approach for structural studies.