A persistence layer for a message exchange system of an application integration system is disclosed. The message exchange system includes a message transport layer configured to transport messages from at least one sending application to one or more receiving applications, and a business process layer configured to execute business process logic on select ones of the messages processed by the message transport layer. The persistence layer is accessible by both the message transport layer and the business process layer, and is configured to store a reference associated with each messages processed by the message transport layer. A system further includes a database accessible from the persistence layer for storing a copy of each messages corresponding to the message references stored in the persistence layer.