The Ta-Li deposit of Orlovka in Eastern Transbaikalia, Russia, is one of the best known rare-metal deposits in cupola-shaped plutons of Li, F-rich rare-metal granites. Quartz from all granite varieties from the deposit was studied using automated mineralogy (TIMA), cathodoluminescence (CL), and laser-ablation inductively-coupled mass spectrometry (LA-ICP MS) in order to find new constraints on the origin of the deposit. Subhedral to euhedral quartz crystals, strongly zoned in CL, relatively enriched in Ti and Li (up to 95 and 33 ppm respectively), and free of mineral inclusions were found in all varieties of biotite granites forming the deeper part of the pluton. Crystals of “snow-ball” quartz with zonally arranged inclusions of albite, with low intensity of CL, and slightly enriched in Al and Ge (up to 350 and 4.8 ppm, respectively) are common in all types of Li-mica granites forming the cupola-shaped upper part of the pluton. The distinction between the two principal types of quartz is generally consistent with the already proposed model of two comagmatic intrusions: deeper-seated biotite granites underwent a complicated magmatic evolution with repeated episodes of crystallization and resorption of quartz, only a limited degree of fractionation, and a small – if any – reaction with fluid. Li-mica granites, taking position within the cupola, strongly fractionated upwards. The upward transfer of Li and rare metals was, moreover, supported by fluid unmixed in the middle level of the cupola.