A series of activated carbons with varied surface chemistry, obtained by wet oxidation and thermal treatment, was used for the removal of penicillin from low concentration aqueous solution. It was found that the carbon surface chemistry favors the degradation of the antibiotic, giving rise to various intermediates detected both in solution and in the adsorbed phase (deposited with the pore structure of the activated carbons). The confinement of penicillin molecules entrapped in the nanopores of activated carbons of acidic nature accelerates their degradation compared to that one in the bulk solution, which can be linked the strong local pH fall inside the pores. Degradation also takes place in activated carbons of basic pH, although the nature and partition of the intermediates formed differ from those in the acidic carbons. In both cases most of the breakdown products do not present therapeutic activity.