Photoluminescence and thermally stimulated luminescence of synthetic and natural (morion and smoky) α-quartz crystals doped with aluminum and alkali ions were studied. The samples were examined both untreated and subjected to substitution of alkali ions for copper or silver ions. The photoluminescence spectrum of the untreated crystals is characterized with the main blue band around 400 nm (~3.1 eV). The corresponding luminescence center is based on a defect containing aluminum and alkali as compensators in natural and synthetic quartz crystals. Photoluminescence is subjected to thermal quenching and can be detected at high temperatures above 700 K, however the main intensity decay takes place at 200 K. The thermal quenching activation energy is 0.15 ± 0.05 eV and the frequency factor is 3·107 s−1. In the samples with silver ions the main luminescence band is located at ~260 nm (~4.7 eV) with a time constant of ~37 μs at 80 K, and in the samples with copper ions the PL band is at ~ 360 nm (~3.4 eV) with a time constant ~ 50 μs at 80 K. The initial luminescence of crystals is greatly reduced after introduction of noble ions. The luminescence of noble ions quenches at 700 K without drop in intensity at 200 K. For luminescence associated with silver the energy of thermal quenching is 0.7 ± 0.1 eV with a frequency coefficient of 1 · 101 3 s−1, and for the luminescence related to copper, these parameters are 0.55 ± 0.1 eV and 1 · 101 2 s−1. The differences in intra-center luminescence properties of the same defect containing alkali ions or noble ions are based on differences in electronic transitions. In the case of alkali ions the charge transfer transitions between oxygen and alkali ions. In the case of noble ions absorption – luminescence corresponds to intra ion transitions. Radiation properties are related to trapping of an electron on one valence ion. Created atom moves out of aluminum containing defect. The hole remains on aluminum-oxygen defect. Thermally stimulated luminescence is related to release of atom, it diffusion to aluminum defect with the hole on oxygen and following radiative recombination. Optically stimulated luminescence is explained by the similar process of optical release of excited atom and movement to aluminum defect and recombination of electron with hole.