The results of studies of the morphology and chemical structure of cobalt coatings deposited by magnetron sputtering on nanostructured surfaces of porous alumina with different morphologies are presented. The morphology of porous alumina was specified by the anodization voltage in solutions of sulfuric (25 V) and oxalic (40 and 120 V) acids. Using scanning electron and atomic force microscopy, it has been shown that the coatings have morphological features, which are hexagonally arranged nanoparticles formed at the boundaries between pores. With an increase in the size of nanopores on the surface of the substrates, the size and shape of the morphological features of the deposited coatings change. According to X-ray absorption fine structure spectroscopy and fine structure spectroscopy of the near region of the X-ray absorption edge, there are changes in the local atomic structure of cobalt, in particular, cobalt in a coating sample deposited on the surface of porous alumina obtained by anodizing at a voltage of 25 V in sulfuric acid, oxidized more strongly, which is associated with greater chemical activity due to the smaller sizes of the nanoparticles that make up the coating. The results obtained will allow in the future to make a directed change in the formation of structure-sensitive properties, such as chemical and electrochemical activity, magnetic sensitivity, of the resulting coatings.