Deterministic real-time multi-protocol heterogeneous packet-based transport is achieved by traffic shaping. When receiving a plurality of packets from a root complex where contents of each packet from the plurality of packets organized in accordance with a first protocol, a sequence number is added to each packet and a packet type is identified. Every packet in the first plurality of packets is encapsulated into at least one packet organized in accordance with a second protocol to form a second plurality of packets organized in accordance with the second protocol. All the packets from the second plurality of packets pass traffic scheduling or traffic shaping prior being sent via a plurality of connections to avoid burstiness and to achieve bounded transport latency in the plurality of connections, thereby providing deterministic real-time behavior in distributed systems.