Fiber Bragg Grating (FBG) sensors are increasing their importance in Structural Health Monitoring (SHM) of composite materials. They excel at reduced size, electromagnetic immunity and corrosion resistance. Furthermore, they are sensitive to strain and temperature, allowing the record of both parameters simultaneously. For the case of composite materials, FBG sensors can be bonded to part surface or embedded within the CFRP plies prior to curing. During the last one, embedded sensors are exposed to high pressure, vacuum and temperature. These conditions modify fiber optic section, causing the degradation of the reflected signal. The received spectrum widens and shows multiple peaks for the same sensor, making signal treatment a complex task. In this paper, an algorithm for peak recognition and monitoring is presented and validated. Embedded sensors included in different set-ups are study through different loading conditions during mechanical testing.