In recent years, the need in security for embedded devices and data centers has increased sharply. The possible consequences of attacks on these equipments make them privileged targets. In these fields, FPGA are increasingly used because of their flexibility and constantly decreasing power consumption and cost: they can embed several hard/soft processors running Linux enhancing system integration. This paper discusses the security issues related to operating system boot security on FPGAs. We show how the software early boot stages can be protected using FPGA built-in security mechanisms and user logic. We consider that external memories can be tampered by software attacks or board level attacks. By using open source elements and standard tools, we present and implement a lightweight solution. We show that the dynamic reconfiguration has nearly no impact on usable resources of the FPGA matrix at the end of the boot process.