Abstract Besides their technological applications, endohedral fullerenes provide ideal conditions for investigating molecular dynamics in restricted geometries. A representative of this class of systems, Sc₃C₂@C₈₀ displays complex intramolecular dynamics. The motion of the ⁴⁵Sc trimer has a remarkable effect on its electron paramagnetic resonance (EPR) spectrum, which changes from a symmetric 22-peak pattern at high temperature to a single broad lineshape at low temperature. The scandium trimer consists of two equivalent and one inequivalent metal atom, due to the carbon dimer rocking through the Sc₃ triangle. We demonstrate through first-principles molecular dynamics (MD), EPR parameter tensor averaging, and spectral modelling that, at high temperatures, three-dimensional movement of the enclosed Sc₃C₂ moiety takes place, which renders the metal centers equivalent and their magnetic parameters effectively isotropic. In contrast, at low temperatures the dynamics becomes restricted to two dimensions within the equatorial belt of the Ih symmetric C₈₀ host fullerene. This restores the inequivalence of the scandium centers and causes their anisotropic hyperfine couplings to broaden the experimental spectrum.