Electron beam induced current (EBIC) at p–n junctions can be measured in high spatial resolution using a thin lamella geometry, where most incident electrons transmit the sample. We explore the case of low excitation energies in a wedge‐shaped lamella geometry to increase resolution in a controlled way. We compare a sample with high (Si) and low (manganite‐titanate heterojunction) diffusion length and use Monte Carlo based simulations as a reference. It is shown that the EBIC signal obtained from the Si junction vanishes below a thickness of 300 nm, whereas this happens at 80 nm in the PCMO–STNO junction. This allows for achieving an EBIC resolution of better than 50 nm for the latter system. The observed fundamental differences between the silicon and the perovskite junction are discussed in terms of preparation induced ‘dead’ layers and surface recombination.