- We present a scheme for cooling a vibrational mode of a magnetic molecular nanojunction by a spin-polarized charge current upon exploiting the interaction between its magnetic moment and the vibration. The spin-polarized charge current polarizes the magnetic moment of the nanoisland, thereby lowering its energy. A small but finite coupling between the vibration and the magnetic moment permits a direct exchange of energy such that vibrational energy can be transferred into the magnetic state. For positive bias voltages, this generates an effective cooling of the molecular vibrational mode. We determine parameter regimes for the cooling of the vibration to be optimal. Although the flowing charge current inevitably heats up the vibrational mode via Ohmic energy losses, we show that due to the magnetomechanical coupling, the vibrational energy (i.e, the effective phonon temperature) can be lowered below 50% of its initial value, when the two leads are polarized anti-parallel. In contrast to the cooling effect for positive bias voltages, net heating of the vibrational mode occurs for negative bias voltages. The cooling effect is enhanced for a stronger anti-parallel magnetic polarization of the leads, while the heating is stronger for a larger parallel polarization. Yet, dynamical cooling is also possible with parallel lead alignments when the two tunneling barriers are asymmetric.