Carbon fibre-reinforced polyetheretherketone (CF-PEEK) composites have gained significant usage across diverse industries like automotive and aerospace due to their desirable characteristics. These properties encompass recyclability, low density, high strength, wear resistance and thermal stability. The components made from CF-PEEK composites for space applications will be subjected to a high radiation environment due to the incoming cosmic rays, comprising protons, α particles, electrons, γ rays, etc., once they escape the Earth’s atmosphere. The ion irradiation of CF-PEEK is accompanied by radiation-induced effects, which drastically change the structure and properties of irradiated material. Since the resistance of CF-PEEK to radiation damage has not been studied extensively, this study aims to understand the effect of high-energy He2+ ions on the microstructure and properties of CF-PEEK composites manufactured using automated fibre placement (AFP) under different processing conditions. The samples have been radiated with 5 MeV He2+ ions using an energy degrader wheel to create a layer with relatively uniform damage. Then, were characterized using optical and scanning electron microscopy and their hardness was evaluated using nanoindentation. It was observed that, irradiation increases the hardness of the fibres in all cases. Also, fibre orientation affects the hardness in a statistically significant manner in both unirradiated and irradiated conditions.