In recent years, the creative use of polymers has been expanded as the range of achievable material properties and options for manufacturing and post-processing continually grows. The main goal of this research was to design and develop a fully-functioning material extrusion additive manufacturing device with the capability to produce functionally graded high-temperature thermoplastic PEEK (polyether ether ketone) materials through the manipulation of microstructure during manufacturing. Five different strategies to control the chamber temperature and crystallinity were investigated, and concepts of thermal control were introduced to govern the crystallisation and cooling mechanics during the extrusion process. The interaction of individually deposited beads of material during the printing process was investigated using scanning electron microscopy to observe and quantify the porosity levels and interlayer bonding strength, which affect the quality of the final part. Functional testing of the printed parts was carried out to identify crystallinity, boundary layer adhesion, and mechanical behaviour. Furnace cooling and annealing were found to be the most effective methods, resulting in the highest crystallinity of the part. Finally, a functionally graded material cylindrical part was printed successfully, incorporating both low and high crystalline regions.