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We report evidence of a non-adiabatic Kohn anomaly in boron-doped diamond, using a joint theoretical and experimental analysis of the phonon dispersion relations. We demonstrate that standard calculations of phonons using density functional perturbation theory are unable to reproduce the dispersion relations of the high-energy phonons measured by high-resolution inelastic x-ray scattering. On the contrary, by taking into account non-adiabatic effects within a many-body field-theoretic framework, we obtain excellent agreement with our experimental data. This result indicates a breakdown of the Born-Oppenheimer approximation in the phonon dispersion relations of boron-doped diamond.