High power SiC MOSFET technologies are critical for energy saving in, e.g., distribution of electrical power. They suffer, however, from low near-interface mobility, the origin of which has not yet been conclusively determined. Here, we present unique concerting evidence for the presence of interface defects in the form of carbon clusters at native thermally processed oxides of SiC. These clusters, with a diameter of 2–5 nm, are HF-etch resistant and possess a mixture of graphitic (sp2) and amorphous (sp3 mixed in sp2) carbon bonds different from the normal sp3 carbon present in 4H-SiC. The nucleation of such defects during thermal oxidation as well as their atomic structure is elucidated by state-of-the-art atomistic and electronic structure calculations. In addition, our property prediction techniques show the impact of the simulated carbon accumulates on the electronic structure at the interface.