The chemical structure of cobalt-polypyrrole - produced by a dual plasma process - is analyzed by means of X-ray photoelectron spectroscopy (XPS), near edge X-ray absorption spectroscopy (NEXAFS), X-ray diffraction (XRD), energy-dispersive X-Ray spectroscopy (EDX) and extended X-ray absorption spectroscopy (EXAFS). It is shown that only nanoparticles of a size of 3 nm with the low temperature crystal structure of cobalt are present within the compound. Besides that, cobalt-nitrogen and carbon-oxygen structures are observed. Furthermore, more and more cobalt-nitrogen structures are produced when increasing the magnetron power. Linking the information on the chemical structure to the results about the catalytic activity of the films - which are presented in part I of this contribution - it is concluded that the cobalt-nitrogen structures are the probable catalytically active sites. The cobalt-nitrogen bond length is calculated as 2.09 angstrom and the carbon-nitrogen bond length as 1.38 angstrom. (C) 2012 The Electrochemical Society. [DOI: 10.1149/2.043209jes] All rights reserved.