Biocompatible nanoparticles possessing persistent luminescence properties offer attractive possibilities for in vivo imaging applications as it allows an excitation of the sensors outside the animal before injection and a long-lasting emission of light. Here we report the development of highly biocompatible calcium phosphate nanoparticles doped with europium, Mn2+ and Ln3+ (Ln3+=Dy3+, Pr3+) ions synthesized by hydrothermal route and tailored to present red-near infrared persistent luminescence after UV excitation. Nanosize biphasic HAp/β-TCP compounds with sphere and rod-shaped were obtained. Two emission bands in the red-near infrared range were observed and attributed to 4T1→6A1 transitions of Mn2+ ions in HAp/β-TCP. An annealing treatment in reductive atmosphere post-synthesis was essential to reveal persistent luminescence properties. Indeed, such thermal treatment allows reducing Eu3+ ions in Eu2+ ions and generating required defaults as oxygen vacancies in the crystal necessary for red emission in accordance with persistent luminescence mechanism. These nanoparticles have been tested for the first time for in vivo imaging on small animal as proof of concept of prospective highly biocompatible nanoprobes.