Technologies for flexible I/O endpoint acceleration include a computing device having a root complex, a soft endpoint coupled to the root complex, and an offload complex coupled to the soft endpoint. The soft endpoint establishes an emulated endpoint hierarchy based on endpoint firmware. The computing device may program the endpoint firmware. The soft endpoint receives an I/O transaction that originates from the root complex and determines whether to process the I/O transaction. The soft endpoint may process the I/O transaction or forward the I/O transaction to the offload complex. The soft endpoint may encapsulate the I/O transaction with metadata and forward the encapsulated transaction to the offload complex. The soft endpoint may store responses from the offload complex in a history buffer and retrieve the responses in response to retried I/O transactions. The I/O transaction may be a PCI Express transaction layer packet. Other embodiments are described and claimed.