Owing to their dynamic phase behaviour and unique gas sorption properties, flexible metal–organic frameworks (MOFs) have emerged as a promising class of materials for applications in gas-related technologies and beyond. Resolving the crystal structures of the distinct phases is essential for understanding their transformation mechanisms and rational tuning framework responsiveness. Here, we revisit the prototypical flexible MOFs ZIF-7 (Zn(bim)₂, bim⁻ = benzimidazolate) and ZIF-9 (Co(bim)₂) and resolve the long-standing ambiguity surrounding their guest-free narrow-pore (np) phases. Using microcrystal three-dimensional electron diffraction combined with powder X-ray diffraction (PXRD) and density functional theory calculations, we determine the crystal structures of both np phases. The results rectify previous structural models and incomplete structural descriptions of the np phase of ZIF-7 and establish the structure of the np phase of ZIF-9. In contrast to the high-symmetry, guest-accommodating large-pore (lp) phases, the np phases adopt distorted, densely packed frameworks with strongly deformed sodalite cages, reduced void fractions, and enhanced framework densities. Variable-temperature PXRD and differential scanning calorimetry further reveal metal-dependent anisotropic thermal expansion of the np phases and entropy-driven np–lp transitions.