Disclosed are various examples for prioritizing application traffic through network tunnels between a client device and a tunnel endpoint. Network traffic is received from each of a plurality of applications executed by the client device. It is determined that the network traffic of a first application of the plurality of applications is associated with a lower priority than the network traffic of a second application of the plurality of applications. A bandwidth allocation to the network traffic of the first application is limited in the encrypted tunnel as compared to a bandwidth allocation to the network traffic of the second application in the encrypted tunnel according to the lower priority. The network traffic of each of the plurality of applications is forwarded through the encrypted tunnel to the tunnel endpoint.