Understanding the role that crystal imperfections or defects play on the physical properties of a solid material is important for any application. In this report, the highly unique crystal structure of the metal–organic framework (MOF) zirconium 2-sulfoterephthalate is presented. This MOF contains a large number of partially occupied ligand and metal cluster sites which directly affect the physical properties of the material. The partially occupied ligand positions give rise to a continuum of pore sizes within this highly porous MOF, supported by N2 gas sorption and micropore analysis. Furthermore, this MOF is lined with sulfonic acid groups, implying a high proton concentration in the pore, but defective zirconium clusters are found to be effective proton trapping sites, which was investigated by a combination of AC impedance analysis to measure the proton conductivity and DFT calculations to determine the solvation energies of the protons in the pore. Based on the calculations, methods to control the pKa of the clusters and improve the conductivity by saturating the zirconium clusters with strong acids were utilized, and a 5-fold increase in proton conductivity was achieved using these methods. High proton conductivity of 5.62 × 10–3 S cm–1 at 95% relative humidity and 65 °C could be achieved, with little change down to 40% relative humidity at room temperature.