Luminescence is a powerful tool to analyse various types of defects in a wide range of materials; it is often applied for silica, which is a broadly used material in photonics, microelectronics, nuclear energy industry, optoelectronics and other important technological applications. In this work, a single crystalline (0001) α-SiO₂ (quartz) sample has been investigated by the ionoluminescence (IL) method. In this case, intense emitted light can be observed when a 2 MeV He⁺ beam reaches the quartz sample. Three emission bands were found at 1.45 eV, 1.76 eV and 2.34 eV, the corresponding defects were identified as an unknown origin, non-bridging oxygen hole centres (NBOHC), and self-trapped excitons (STEs), respectively. The evolution of the defect-related IL peaks was determined as a function of He⁺ irradiation fluence. To perform accurate data evaluation, the instrumental function of the applied IL set-up (collimator, optical fibers and spectrometer) was determined and taken into account. The importance of methodological issues in the IL measurement (including set-up, sample holder and proper beam settings) was also discussed. The described steps of system calibration and data evaluation are indispensable for IL spectrum analysis leading to a detailed understanding of defect evolution taking place during the ion-beam irradiation process.