Multi-stage treatment methods for the treatment or removal of iron sulfide scales in subterranean operations and operations involving the production and/or transportation of oil and gas. In one embodiment, the methods include identifying one or more types of iron sulfide scale present in a portion of a subterranean formation; introducing a first treatment composition comprising an acid into at least a portion of the subterranean formation to partially dissolve the iron sulfide scale therein; and introducing a second treatment composition into the portion of the subterranean formation after the first treatment composition, the second treatment composition comprising an iron sulfide treating additive selected based at least in part on a type of iron sulfide scale identified in the subterranean formation.