A density functional theory study of the elementary steps that lead to the removal of COads(Pt) over alloyed and sequentially deposited Pt/Ru bimetallic nanoclusters is presented. The reaction energies and activation barriers for the H2Oads(Ru) dissociation and COads(Pt) + OHads(Ru) reaction are estimated in solid-gas interface and in a microsolvated environment to determine which surface morphology is more tolerant to COads poisoning. On the basis of the energetics, the sequentially deposited Pt/Ru nanocluster is predicted to be a much more promising anode catalyst than the alloy cluster surface in fuel cell applications.