The guest-dependent flexibility of the pillared-layered metal-organic framework (MOF), Zn2bdc2dabco·X(guest), where guest = EtOH, DMF or benzene, has been examined by high-pressure single crystal X-ray diffraction. A pressure-induced structural phase transition is found for the EtOH- and DMF-included frameworks during compression in a hydrostatic medium of the guest species, which is dependent upon the nature and quantity of the guest in the channels. The EtOH-included material undergoes a phase transition from P4/mmm to C2/m at 0.69 GPa, which is accompanied by a change in the pore shape from square to rhombus via super-filling of the pores. The DMF-included material undergoes a guest-mediated phase transition from I4/mcm to P4/mmm at 0.33 GPa via disordering of the DMF guest. In contrast, the benzene-included framework features a structure with rhombus-shaped channels at ambient pressure and shows direct compression under hydrostatic pressure. These results demonstrate the large influence of guest molecules on the high-pressure phase behavior of flexible MOFs. Guest-mediated framework flexibility is useful for engineering MOFs with bespoke pore shapes and compressibility.