A persistent problem for modern Multi-Processors System-on-Chip (MPSoCs) is their vulnerability to code injection attacks. By tampering the memory content, attackers are able to extract secrets from the MPSoC and to modify or deny the MPSoC’s operation. This work proposes SEPUFSoC (Secure PUF-based SoC), a novel flexible, secure, and fast architecture able to be integrated into any MPSoC. SEPUFSoC prevents execution of unauthorized code as well as data manipulation by ensuring memory integrity and authentication. SEPUFSoC achieves: i) efficiency, through the integration of a fast and lightweight hash function for Message Authentication Code (MAC) generation and integrity verification of the memory lines at runtime; and ii) lightweight security, through the use of a Physical Unclonable Function (PUF) to securely generate and store the cryptographic keys that are used for the application authentication. We discuss the security and performance of SEPUFSoC for single core and multi-core systems. Results show that the SEPUFSoC is a secure, fast, and low overhead solution for MPSoCs. We discuss the SEPUFSoC security and cost, which strongly depends on the PUF and hash selection. In the future, new technologies may allow the exploration of different PUFs.