Nowadays, 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene – better known as BODIPY – is at the forefront of fluorophores for life sciences. Indeed, its high brightness, its tunable excitation and emission wavelengths along with its high chemical and photochemical stability draw more and more the interest of researchers. In the last decade, chemists have taken advantage of the versatility of the synthesis of BODIPY to design sophisticated objects. This review focuses on the different recent studies dealing with the conception of metal-based-BODIPY derivatives for medical purposes. More precisely, emphasis is put on the use of BODIPY derivatives for the elaboration of BODIPY-based theranostics, multimodal imaging probes, and photodynamic therapy sensitizers.