DUT-8(Ni) metal–organic framework (MOF) belongs to the family of flexible pillared layer materials. The desolvated framework can be obtained in the open pore form (op) or in the closed pore form (cp), depending on the crystal size regime. In the present work, we report on the behaviour of desolvated DUT-8(Ni) at elevated temperatures. For both, op and cp variants, heating causes a structural transition, leading to a new, crystalline compound, containing two interpenetrated networks. The state of the framework before transition (op vs. cp) influences the transition temperature: the small particles of the op phase transform at significantly lower temperature in comparison to the macroparticles of the cp phase, transforming close to the decomposition temperature. The new compound, confined closed pore phase (ccp), was characterized by powder X-ray diffraction and spectroscopic techniques, such as IR, EXAFS, and positron annihilation lifetime spectroscopy (PALS). Thermal effects of structural transitions were studied using differential scanning calorimetry (DSC), showing an overall exothermic effect of the process, involving bond breaking and reformation. Theoretical calculations reveal the energetics, driving the observed temperature induced phase transition.