The Fused Filament Fabrication (FFF) process of polyether(ether ketone), PEEK, is a challenging task due to its high melting point and viscosity that imply the need of high temperature of printing and the optimization of many process parameters. In the present work, the influence of printing speed, nozzle and chamber temperature on both crystalline and mechanical tensile characteristics was evaluated. The results showed the possibility to control the 3D-printed PEEK structural properties on which the tensile performances strongly depend. In particular, it was found that the chamber temperature is the parameter that most influences the specimens crystallinity degree which determines their actual tensile behavior. The higher the degree of crystallinity, the stiffer the material is. Furthermore, the printing speed and nozzle temperature play a key role in reducing voids inside the printed parts, thereby increasing tensile strength. In this work, the best tensile performance and the higher degree of crystallinity were obtained by keeping the chamber temperature of 160°C, the nozzle temperature of 450°C and the printing speed of 1500 mm/min. Thus, according to the final application of the printed parts, a careful choice of these parameters is needed.