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The functionalization of endohedral metallofullerenes by halogenation has not been previously reported and remains a challenging endeavor in carbon nanoscience. In this work, we show that halogenation of endohedral metallofullerenes is predicted to be feasible based on thermodynamic grounds by means of DFT computations, combined with in situ experimental investigations. Computed bond energies for the chlorination, fluorination and hydrogenation of endohedral metallofullerenes that span a range of cage sizes are found to be comparable to those of known halogenated and hydrogenated empty fullerenes. Therefore, we propose that new forms of functionalized metallofullerenes should be synthesized under appropriate experimental conditions, despite many prior unsuccessful attempts. Indeed, we experimentally show for the first time that M@C2n (M = metal) metallofullerenes and the prototypical Sc3N@C80 clusterfullerene can be fluorinated by two different routes under the typical ‘harsh’ gas phase conditions of metallofullerene plasma synthesis, and at lower extents that could avoid cage degradation. The combination of halogenation and metal encapsulation offers the potential to create new radical-quenched, functionalized endohedral metallofullerenes that possess stable, large-gap carbon cages. These results open new avenues for the synthesis and stabilization of encapsulated molecular nanocarbons.