Among redox sensitive elements, carbon is particularly important because it may have been a driver rather than a passive recorder of Earth’s redox evolution. The extent to which the isotopic composition of carbon records the redox processes that shaped the Earth is still debated. In particular, the highly reduced deep mantle may be metal-saturated, however, it is still unclear how the presence of metallic phases influences the carbon isotopic compositions of super-deep diamonds. Here we report ab initio results for the vibrational properties of carbon in carbonates, diamond, and Fe3C under pressure and temperature conditions relevant to super-deep diamond formation. Previous work on this question neglected the effect of pressure on the equilibrium carbon isotopic fractionation between diamond and Fe3C but our calculations show that this assumption overestimates the fractionation by a factor of ~1.3. Our calculated probability density functions for the carbon isotopic compositions of super-deep diamonds derived from metallic melt can readily explain the very light carbon isotopic compositions observed in some super-deep diamonds. Our results therefore support the view that metallic phases are present during the formation of super-deep diamonds in the mantle below ~250 km.