We demonstrate an unusual crystal-structure transition from metal–organic frameworks (MOFs) composed of ortho-phthalate ligands. The time-course change observed in X-ray diffraction experiments showed that the continuous structural transformation of MOFs occurs after immersion in N,N-dimethylformamide solution containing ortho- or para-tetrafluorophthalate ligands. Systematic study based on single crystal X-ray analysis reveals that the structural strain in the metal–ligand coordination network is a crucial factor in the potential of the metal center to undergo partial bond dissociation and ligand substitution.