The study documents changes in the chemical composition of igneous quartz during evolution of two contrasting late-Variscan granite suites in the Erzgebirge/Krušné Hory Mts., Czech Republic. Quartz is the chemically most resistant rock-forming mineral in granitoids, so trace-element signatures in quartz preserve its magmatic character during all common post-magmatic alterations. Six quartz populations were optically distinguished in each of the studied granite suites: a highly peraluminous phosphorus-rich (S-type) from Podlesí, and slightly peraluminous P-poor (A-type) from Hora Svaté Kateřiny. Contents of Li, Be, B, Al, Ge, P, K, Na, Ca, Ti, Mn, and Fe were determined in situ in all quartz types using laser ablation inductively coupled plasma mass spectrometry, LA-ICP-MS. Of all the determined elements, only Ti decreases with increasing fractionation. Al reached the highest contents in all samples (100–1200 μg g−1), followed by Ti, Li, and K (in the range of 10–100 μg g−1). The Ti vs. Al diagram is the most fitting indicator of the evolution of the melt from which the quartz crystallised. Al enters the quartz lattice according to coupled substitution Si4+ ↔ Al3+ + (Li, K, H)+. No first-hand correlation between Al in quartz and the peraluminosity of the melt was found. Contents of Al increase from the early to the late quartz populations, by factors of 3 in Podlesí and 10 in Katerina, despite the aluminium saturation index of both granite systems increasing only slightly or becoming stable: 1.20–1.35 in Podlesí and 1.05 in Katerina. The contents of B, Be, Ge, Fe, Mn, and P in quartz are usually lower than 10 μg g−1 and their abundances are generally positively correlated with whole-rock chemical compositions. Erratic, high contents of Fe and Mn in quartz from marginal pegmatite may be attributed to infiltration of fluid from the exocontact during quartz crystallisation.