Xenon (Xe), the heaviest of the stable noble gases, is missing by a factor of 20 relatively to other noble gases, when comparing the Earth’s and Mars’s atmospheres with chondrites. In this work, the possibility of Xe retention in quartz, a major mineral of the continental crust is tested. The Xe-SiO2 system is investigated from 0.7 GPa to 2.7 GPa and up to 1900 K, by in situ X-ray powder diffraction and infrared spectroscopy. Experimental data are complemented by ab initio calculations to retrieve Xe incorporation mechanisms. An excess of quartz unit-cell volume up to 4.2 % is observed, consistent with a Xe for Si substitution in the quartz structure. Xe has a linear oxygen environment composed of two O atoms located at 1.98-2.00 Å from the Xe atom. Moreover, a new phase is evidenced above Xe melting curve at 0.8-1.0 GPa. The new (Xe,Si)O2 phase is orthorhombic and corresponds to an elongation of the quartz unit-cell. In this phase, Xe substitutes for Si with a nearly planar oxygen environment composed of four O atoms located at 2.06-2.09 Å from the Xe atom. Xe incorporation in SiO2 proves to be significant, as previously shown for olivine. Xe incorporation is therefore expected to occur in the whole range of lithospheric silicate minerals. These findings emphasize the need to consider Xe incorporation in crust and upper mantle minerals as a process to store and fractionate xenon, in the framework of the ‘missing xenon’ issue.