A carbon-fibre reinforced carbon-matrix (C/C) composite was irradiated with 30 MeV C6+ ions to a peak damage of ∼25 dpa. Ion irradiation-induced microstructural changes were mainly studied using Raman spectroscopy. The irradiation-induced crystal lattice defect accumulation in the C/C composite was compared with a reference of PCIB graphite (nuclear-grade). It shows that a high concentration of pre-existing crystal lattice defects in the studied C/C composite have a significant impact on the unexpectedly high disordering of the crystal lattice observed along the entire ion range. In comparison, PCIB graphite with much less pre-existing crystal lattice defects behaves in a more predictable manner with the irradiation damage accumulated in a narrow high dpa region. We rationalised that a large number of pre-existing crystal lattice defects in the C/C composite lead to a stronger electron-phonon coupling and play an important role on the formation of stable crystal lattice defects due to electronic energy loss during ion irradiation. The present results have implications for the development of C/C composites for radiation-tolerant applications, in terms of the crystal lattice defect elimination in the as-manufactured microstructure. Additionally, this investigation identifies a fundamental knowledge gap in the electronic energy loss effect on the irradiation damage produced in carbon-based materials at intermediate ion energies.