We show how the structural order of nanocrystalline zirconium phosphates (ZrP) is tuned by the synthetic methods and conditions through the use of synchrotron X-ray atomic pair distribution function analysis. With different synthetic route and different phosphoric acid concentrations in the synthesis, the product zirconium phosphates vary from turbostratically disordered nanoscale structures to fully ordered ones. We show that a change in the structural order leads to different ion-exchange properties. The samples are characterized using multiple techniques, including powder X-ray diffraction, ion exchange, thermogravimetric analysis, transmission electron microscopy, fast neutron activation analysis, solid-state NMR spectroscopy, IR spectroscopy, and X-ray photoelectron spectroscopy.