We report on the tuning of the Kondo effect in thin Au films containing a monolayer of cobalt(II) terpyridine complexes by altering the ligand structure around the Co(2+) ions by depositing a thin Au capping layer on top of the monolayer on Au by magnetron sputtering (more energetic) and e-beam evaporation (softer). We show that the Kondo effect is slightly enhanced with respect to that of the uncapped film when the cap is deposited by evaporation, and significantly enhanced when magnetron sputtering is used. The Kondo temperature (TK) increases from 3 to 4.2/6.2 K for the evaporated/sputtered caps. X-ray absorption spectroscopy and surface-enhanced Raman spectroscopy investigation showed that the organic ligands remain intact upon Au e-beam evaporation; however, sputtering inflicts significant change in the Co(2+) electronic environment. The location of the monolayer-on the surface or embedded in the film-has a small effect. However, the damage of Co-N bonds induced by sputtering has a drastic effect on the increase of the impurity-electron interaction. This opens up the way for tuning of the magnetic impurity states, e.g. spin quantum number, binding energy with respect to the host Fermi energy, and overlap via the ligand structure around the ions.