Dynamic partial reconfiguration is a growing need for SRAM FPGA-based embedded systems. This feature allows reconfiguring parts of the FPGA while others continue to run. But it may introduce security breaches affecting FPGA configuration. In this paper, a secure protocol to ensure confidentiality, integrity, authenticity and up-to-dateness is described and applied to dynamic partial reconfiguration. Two common threat models are addressed for industrially-driven use cases. The implementation can perform both secure update and reconfiguration without significantly affecting performances.