Heating of quartz crystals in order to study melt and high-temperature fluid inclusions is a common practice to constrain major physical and chemical parameters of magmatic and hydrothermal processes. Diffusion and modification of trace element content in quartz and its hosted melt inclusions have been investigated through step-heating experiments of both matrix-free quartz crystals and quartz crystals associated with sulfides and other minerals using a Linkam TS1500 stage. Magmatic and hydrothermal quartz were successively analyzed after each heating step for Cu, Al, and Ti using electron probe micro-analyzer. After the last heating step, quartz crystals and their hosted melt inclusions were analyzed by laser ablation inductively coupled plasma mass spectrometry and compared to unheated samples. Heated samples reveal modification of Cu, Li, Na, and B contents in quartz and modification of Cu, Li, Ag, and K concentrations in melt inclusions. Our results show that different mechanisms of Cu, Li, and Na incorporation occur in magmatic and hydrothermal quartz. Heated magmatic quartz records only small, up to a few ppm, enrichment in Cu and Na, mostly substituting for Li. By contrast, heated hydrothermal quartz shows enrichment up to several hundreds of ppm in Cu, Li, and Na, which substitute for originally present H. This study reveals that the composition of both quartz and its hosted melt inclusions may be significantly modified upon heating experiments, leading to erroneous quantification of elemental concentrations. In addition, each quartz crystal also becomes significantly enriched in Cu in the sub-surface layer during heating. We propose that sub-surface Cu enrichment is a direct indication of Cu diffusion in quartz externally sourced from both the surrounding sulfides as well as the copper pins belonging to the heating device. Our study shows that the chemical compositions of both heated quartz and its hosted inclusions must be interpreted with great caution to avoid misleading geological interpretations.