Biomineralization consists of a complex cascade of phenomena generating hybrid nano-structured materials based on organic (e.g., polymer) and inorganic (e.g., hydroxyapatite) components. Biomineralization is a biomimetic process useful to produce highly biomimetic and biocompatible materials resembling natural hard tissues such as bones and teeth. In detail, biomimetic materials, composed of hydroxyapatite nanoparticles (HA) nucleated on an organic matrix, show extremely versatile chemical compositions and physical properties, which can be controlled to address specific challenges. Indeed, different parameters, including (i) the partial substitution of mimetic doping ions within the HA lattice, (ii) the use of different organic matrices, and (iii) the choice of cross-linking processes, can be finely tuned. In the present review, we mainly focused on calcium biomineralization. Besides regenerative medicine, these multifunctional materials have been largely exploited for other applications including 3D printable materials and in vitro three-dimensional (3D) models for cancer studies and for drug testing. Additionally, biomineralized multifunctional nano-particles can be involved in applications ranging from nanomedicine as fully bioresorbable drug delivery systems to the development of innovative and eco-sustainable UV physical filters for skin protection from solar radiations.