Peroxide ions in apatite provides an additional resource for imparting an antibacterial capability in apatite. A hydrothermal process has been developed for including peroxide ions into the apatite lattice. Three oxygen generating compounds (hydrogen peroxide, ammonium persulphate and peracetic acid) were investigated for generating peroxyapatite. Hydrogen peroxide provides the highest peroxide containing apatite. Both the oxygen generation and crystallization of apatite represented the two critical factors for producing peroxyapatite. Unlike with high temperature processing, the cooling rate did not influence the retained peroxide content. This new process provides a building block for investigating antibacterial properties of peroxyapatite produced by a low temperature process.