Endohedral clusters in metallofullerenes can vary in a broad range of geometrical parameters following the size and shape of the host carbon cage. Obviously, distortions of the cluster may increase its energy and even destabilize the whole clusterfullerene molecule. However, direct evaluation of the magnitude of cluster strain energies has not been done because of the lack of a suitable computational scheme that would allow one to decouple cluster and fullerene distortions and hence estimate individual components. In this work we offer a simple and efficient scheme to calculate cluster distortion energies in endohedral metallofullerenes (EMEs). Using this scheme, we analyze distortions in three classes of EMFs with nitride, sulfide, and carbide clusters and different metal atoms (Sc, Y, Ti).