We investigate cooling of a vibrational mode of a magnetic quantum dot by a spin-polarized tunneling charge current exploiting the magnetomechanical coupling. The spin-polarized current polarizes the magnetic nanoisland, thereby lowering its magnetic energy. At the same time, Ohmic heating increases the vibrational energy. A small magnetomechanical coupling then permits us to remove energy from the vibrational motion and cooling is possible. We find a reduction of the vibrational energy below 50% of its equilibrium value. The lowest vibration temperature is achieved for a weak electron-vibration coupling and a comparable magnetomechanical coupling. The cooling rate increases at first with the magnetomechanical coupling and then saturates.