We present an unambiguous identification of low-frequency terahertz vibrations in the archetypal imidazole-based metal-organic framework (MOF) materials: ZIF-4, ZIF-7, and ZIF-8, all of which adopt a zeolite-like nanoporous structure. Using inelastic neutron scattering and synchrotron radiation far-infrared absorption spectroscopy, in conjunction with density functional theory (DFT), we have pinpointed all major sources of vibrational modes. Ab initio DFT calculations revealed the complex nature of the collective THz modes, which enable us to establish detailed correlations with experiments. We discover that low-energy conformational dynamics offers multiple pathways to elucidate novel physical phenomena observed in MOFs. New evidence demonstrates that THz modes are intrinsically linked, not only to anomalous elasticity underpinning gate-opening and pore-breathing mechanisms, but also to shear-induced phase transitions and the onset of structural instability.