The present invention relates to pharmaceutical compositions and methods for the treatment of peri-implant diseases, in particular peri-implant disease characterized by the destruction of the crest of the alveolar bone supporting the implant. Specifically, the method comprising the step of applying to a peri-implant bone displaying crestal resorption a 5 pharmaceutical composition comprising biocompatible bone augmentation material coated with a matrix composition which provides local controlled and prolonged release of at least one pharmaceutically active agent at the bone loss site.