Methods and systems are provided for increasing application performance and accelerating data communications in a WAN environment. According to one embodiment, packets are received at a flow classification module operating at the Internet Protocol (IP) layer of a first wide area network (WAN) acceleration device via a private tunnel, which is operable to convey application layer data for connection-oriented applications between WAN acceleration devices. The packets are passed to a WAN socket operating at the transport layer. Based on the application protocol, the packets are passed to an application handler of multiple application handlers operating at the application layer each of which implements one or more application acceleration techniques for a particular application layer protocol known to behave poorly within a WAN environment. The existing connection-oriented flow is securely accelerated by performing one or more application acceleration techniques and applying one or more security functions.