The origin of yellow cathodoluminescence (CL) in quartz has been investigated by a combination of CL microscopy and spectroscopy, electron paramagnetic resonance (EPR) spectroscopy, and spatially resolved trace-element analysis by laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS). The study shows that the appearance of a ~570 nm (2.17 eV) emission band can be attributed to high oxygen deficiency and local structural disorder in quartz. A proposed luminescence center model implies self-trapped exciton (STE) emission from localized amorphized regions in quartz. Although the high-intensity emission at 570 nm is in general consistent with high concentrations of E′1 defects detected by EPR spectroscopy, CL studies with different electron beam parameters and annealing experiments up to 600 °C show a temperature and irradiation dependence of the luminescence related defects excluding the role of E′1 centers as direct luminescence activators for the 570 nm emission. The evaluation of geochemical data shows that quartz with yellow CL occurs in low-temperature hydrothermal environment (mostly <250 °C) and is related to fast crystallization in an environment with oxygen deficiency.