Methods for forming cobalt silicide are provided. One method for forming a cobalt silicide material includes exposing a substrate having a silicon-containing material to either a wet etch solution or a pre-clean plasma during a first step and then to a hydrogen plasma during a second step of a pre-clean process. The method further includes depositing a cobalt metal layer on the silicon-containing material by a CVD process, heating the substrate to form a first cobalt silicide layer comprising CoSi at the interface of the cobalt metal layer and the silicon-containing material during a first annealing process, removing any unreacted cobalt metal from the substrate during an etch process, and heating the substrate to form a second cobalt silicide layer comprising CoSi2 during a second annealing process.