The relation between the atomic hybridization and the secondary electron emission yield (SEY) in carbon materials has been investigated during the thermal graphitization of thin amorphous carbon layers deposited by magnetron sputtering on Cu substrates. Cl s core level, valence band and Raman spectroscopy were used to follow the sp(3 ->)sp(2) structural reorganization while the SEY curves as a function of the kinetic energy of the incident electron beam were measured in parallel. We found that an amorphous C layer with a thickness of a few tens of nanometers is capable to modify the secondary emission properties of the clean copper surface, reducing the maximum yield from 1.4 to 1.2. A further SEY decrease observed with the progressive conversion of sp3 hybrids into six-fold aromatic domains was related to the electronic structure close to the Fermi level of the C-films. We found that a moderate structural quality of the C layer is sufficient to notably decrease the SEY as aromatic clusters of limited size approach the secondary emission properties of graphite. (C) 2014 Elsevier B.V. All rights reserved.