A tool for depositing multilayer coatings onto a substrate. In one configuration, the tool includes a includes an in-line organic material deposition station operating under at least one of a pressure or temperature controlled environment. In another, it further is of a hybrid design that incorporates both in-line and cluster tool features. In this latter configuration, at least one of the deposition stations is configured to deposit an inorganic layer, while at least one other deposition station is configured to deposit an organic layer. The tool is particularly well-suited to depositing multilayer coatings onto discrete substrates, as well as to encapsulating environmentally-sensitive devices placed on the flexible substrate.