A tool for depositing multilayer coatings onto a substrate. The tool includes a housing defining a vacuum chamber connected to a vacuum source, deposition stations each configured to deposit a layer of multilayer coating on the substrate, a curing station, and a contamination reduction device. 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. In one tool configuration, the substrate may travel back and forth through the tool as many times as needed to achieve the desired number of layers of multilayer coating. In another, the tool may include numerous housings adjacently spaced such that the substrate may make a single unidirectional pass. The contamination reduction device may be configured as one or more migration control chambers about at least one of the deposition stations, and further includes cooling devices, such as chillers, to reduce the presence of vaporous layer precursors. The tool is particularly well-suited to depositing multilayer coatings onto flexible substrates, as well as to encapsulating environmentally-sensitive devices placed on the flexible substrate.