FeCo-alloy graphite-coated nanoparticles with mean particle diameter under 8 nm have been synthesized following a CVD carbon-deficient method. The superior magnetic properties of FeCo-alloy nanoparticles makes them good candidates to be used as magnetic filler in magneto-polymer composites. Thanks to the protective effect of the graphite shell, FeCo nanoparticles are stable under oxygen atmosphere up to 200 ° C. The as-prepared nanoparticles presented a highly long range chemically ordered core being ferromagnetic at room temperature with a saturation magnetization at room temperature close to the bulk value. After annealing at 750 K the saturation magnetization and the coercive field increase. To investigate the processes involved in the thermal treatment, the temperature dependence of the magnetization and the particle composition, size and structure have been characterized before and after annealing. Besides powder x-ray diffraction (XRD) and x-ray photoelectron spectroscopy (XPS), a detailed study by means of advanced transmission electron microscopy (TEM) techniques has been carried out. In particular, aberration corrected scanning transmission electron microscopy (STEM), has shown that nanoparticles became faceted after the thermal treatment, as a mechanism to reach the thermodynamic equilibrium within the metastable phase. This outstanding feature, not previously reported, leads to an increase of the shape anisotropy, which in turn might be the origin of the observed increase of the coercive field after annealing.