A coated article is provided that may be used as a vehicle windshield, insulating glass (IG) window unit, or the like. Ion beam treatment is performed on a layer(s) of the coating. For example, a silicon nitride layer of a low-E coating may be ion beam treated. It has been found that ion beam treatment, for example, of a silicon nitride underlayer is advantageous in that sodium migration from the glass substrate toward the IR reflecting layer(s) can be reduced during heat treatment.