Computing apparatus includes a central processing unit (CPU), which is configured to run concurrently multiple virtual machines, including at least first and second virtual machines. A peripheral component bus is connected to communicate with the CPU. Multiple peripheral devices are connected to communicate via the bus with the CPU and with others of the peripheral devices, including at least first and second peripheral devices that are each respectively partitioned into at least first and second functional entities, which are respectively assigned to serve the at least first and second virtual machines. Access control logic is configured to forward peer-to-peer communications initiated by the functional entities between the peripheral devices over the bus while inhibiting access in the peer-to-peer communications between the functional entities that are assigned to different ones of the virtual machines.