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, wherein the substrate at the first processing position is at a first temperature; (c) rotating the substrate to a second processing position; and (d) annealing the substrate at the second processing position to remove contaminants from the cobalt layer, wherein the substrate at the second processing position is at a second temperature greater than the first temperature.