With the development of ultralow-dose (scanning) transmission electron microscopy ((S)TEM) techniques, atomic-resolution imaging of highly sensitive nanomaterials has recently become possible. However, applying these techniques to the study of sensitive bulk materials remains challenging due to the lack of suitable specimen preparation methods. We report that cryogenic focused ion beam (cryo-FIB) can provide a solution to this challenge. We successfully extracted thin specimens from metal-organic framework (MOF) crystals and a hybrid halide perovskite single-crystal film solar cell using cryo-FIB without damaging the inherent structures. The high quality of the specimens enabled the subsequent (S)TEM and electron diffraction studies to reveal complex unknown local structures at an atomic resolution. The obtained structural information allowed us to resolve planar defects in MOF HKUST-1, three-dimensionally reconstruct a concomitant phase in MOF UiO-66, and discover a new CH3NH3PbI3 structure and locate its distribution in a single-crystal film perovskite solar cell. This proof-of-concept study demonstrates that cryo-FIB has a unique ability to handle highly sensitive materials, which can substantially expand the range of applications for electron microscopy.