A network interface device includes a bus interface that communicates over a bus with a host processor and memory, and a network interface that sends and receive data packets carrying data over a packet network. A protocol processor conveys the data between the network interface and the memory via the bus interface while performing protocol offload processing on the data packets in accordance with multiple different application flows. The bus interface queues the data for transmission over the bus in a plurality of queues that are respectively assigned to the different application flows, and transmits the data over the bus according to the queues.