Embedded systems are used in several domains and are parts of our daily life : we use them when we use our smartphones or when we drive our modern cars embeddingGPS, light/rain sensors and other electronic assistance mechanisms. These systems process sensitive data (such as credit card numbers, critical information about the host system and so on) which must be protected against external attacks as these data are transmitted through a communication link where the attacker can connect to extract sensitive information or inject malicious code within the system. Unfortunately, embedded systems containmore andmore components which make more and more security breaches that can be exploited to provoke attacks. One of the goals of this thesis is to propose a method to protect communications and memories in a multiprocessor architecture implemented in a FPGA reconfigurable chip. The method is based on the implementation of hardware mechanisms offering monitoring and cryptographic features in order to give a secured execution environment according to a given threat model. The main goal of the solution proposed in this work is to minimize perturbations in the data traffic ; it is considered that it can be accomplished by focusing on the latency impact of our security mechanisms. Our solution is also sensible to attack events : as soon as an attack is detected, an update process of security policies can be enabled. Following an analysis of implementation results, two extensions of the basic solution are described : a fully-secured flow for startup/maintenance of FPGA-based multiprocessor systems and a method to improve attacks detection in order to take into account software parameters in multitasks applications.