Quartz and carbonaceous materials, which are used in the production of silicon as well as electrodes and refractories in the silicon furnace, contain trace elements mostly in the form of oxides. These oxides can be reduced to gaseous compounds and leave the furnace or stay in the reaction products—metal and slag. This article examines the behavior of trace elements in hydrothermal quartz and quartzite in the reaction of SiO2 with Si or SiC. Mixtures of SiO2 (quartz or quartzite), SiC, and Si in forms of lumps or pellets were heated to 1923 K and 2123 K (1650°C and 1850°C) in high purity graphite crucibles under Argon gas flow. The gaseous compounds condensed in the inner lining of the tube attached to the crucible. The phases present in the reacted charge and the collected condensates were studied quantitatively by X-ray diffraction (XRD) and qualitatively by Electron Probe Micro Analyzer (EPMA). Contaminants in the charge materials, reacted charge and condensate were analyzed by Inductively Coupled Plasma-Mass Spectroscopy (ICP-MS). Muscovite in the mineral phase of quartz melted and formed two immiscible liquid phases: an Al-rich melt at the core of the mineral, and a SiO2-rich melt at the mineral boundaries. B, Mn, and Pb in quartz were removed during heating in reducing atmosphere at temperature above 1923 K (1650°C). Mn, Fe, Al and B diffused from quartz into silicon. P concentration was under the detection limit. Quartzite and hydrothermal quartz had different initial impurity levels: quartzite remained more impure after reduction experiment but approached purity of hydrothermal quartz upon silica reduction.