Host–guest chemistry in microporous crystals underpins key applications in catalysis1, separation2 and sensing3, yet the unambiguous identification of guest species within host frameworks remains a central challenge. Recent advances in low-dose phase-contrast electron microscopy have enabled real-space imaging of guest moieties and transformed this field4,5. Here, however, we show that standard implementations of these techniques can generate artefactual in-pore contrast owing to non-ideal contrast transfer, thus compromising the reliability of guest identification. We address this limitation with a reconstruction method based on Gaussian-apodized single-sideband electron ptychography, which suppresses such artefacts and yields chemically interpretable phase images. We apply this method to an important catalytic system, achieving unbiased identification of guest metal–oxo clusters within microporous zeolite hosts. Our results are supported by complementary diffraction and spectroscopy. Beyond revealing previously unreported framework-confined metal active sites in zeolites, this method is expected to enable high-fidelity visualization of a broad range of local inhomogeneities across crystalline porous materials.
