Methods and apparatus for depositing a cobalt layer in features formed on a substrate are provided herein. In some embodiments, a method of depositing a cobalt layer atop a substrate includes: (a) providing a substrate to a substrate support that is rotatable between two processing positions; (b) exposing the substrate to a cobalt containing precursor at a first processing position to deposit a cobalt layer atop the substrate; (c) rotating the substrate having the deposited cobalt layer to a second processing position; and (d) treating the substrate at the second processing position to remove contaminants from the cobalt layer.