The present subject matter relates to systems and methods for sealing one or more MEMS devices within an encapsulated cavity. A first material layer can be positioned on a substrate, the first material layer comprising a first cavity and a second cavity that each have one or more openings out of the first material layer. At least the first cavity can be exposed to a first atmosphere and sealed while it is exposed to the first atmosphere while not sealing the second cavity. The second cavity can then be exposed to a second atmosphere that is different than the first atmosphere, and the second cavity can be sealed while it is exposed to the second atmosphere.