Synthetic bone grafts that promote the natural mineralization process are excellent candidates for the repair and replacement of bone defects. In this study, a series of phosphoester and phosphonic acid containing polyphosphazenes were examined for their ability to mineralize hydroxyapatite (HAp) during exposure to a solution of simulated body fluid (SBF) for a period of four weeks. Although all the polymers showed an initial mineralization response, the amount of deposition and the time scale were dependent upon the side group chemistry of the polymers. After exposure to SBF for one week, all polymers mineralized HAp. After three weeks in SBF, polymers containing phosphoester substituents showed no significant change, with a weight gain of <1%, while polymers containing phosphonic acid substituents underwent a significant increase in the amount of mineralized HAp, with weight gains between 5–10%. The morphology of mineralized features was observed with Environmental Scanning Electron Microscopy (ESEM). However, due to the structural complexity of the mineralized polymers, the identity of the mineralized phase could not be definitively identified using traditional characterization techniques such as energy dispersive spectroscopy (EDS), X-ray diffraction (XRD), Fourier-transform infrared spectroscopy (FTIR), or X-ray photoelectron spectroscopy (XPS). Time-of-flight secondary ion mass spectrometry (ToF-SIMS), a technique not previously explored for this type of application, successfully reveals details of the chemistry associated with the mineralized phase not possible to achieve with XRD analysis.