Multiple independent endpoint devices can be emulated using a single system on chip (SoC) device. Such a SoC can have multiple cores that can emulate ports according to a specified protocol, such as the peripheral component interconnect express (PCIe) protocol useful for data communications. An emulation agent can manage various aspects of these emulated endpoint devices in software, including serving interrupts for relevant emulated devices according to a determined priority scheme. Interrupts can be registered for each device, and data structures allocated dynamically for a determined number and type(s) of PCIe endpoint devices to be emulated. Each PCIe core on the SoC can function as a separate PCIe endpoint device endpoint for communicating with one or more hosts or other such devices.