In this study, we present the first systematic dataset on natural variations of OH defect and trace element contents in quartz within igneous bodies. Samples were derived from bore holes of two plutonic bodies from the Krušné Hory/Erzgebirge (German–Czech border), representing typical A-type (Cínovec/Zinnwald granite cupola) and S-type (Podlesí Stock) granite intrusions. Fourier Transform Infrared spectroscopy of quartz was used to investigate the sample set with regard to its OH defect speciation and content. For Zinnwald quartz, IR absorption spectra reveal different lithologies due to changes of the OH defect inventory, enabling a subdivision of the granitic body: (1) hydrothermal greisen quartz of the uppermost part of the intrusion have low OH defect contents (average of 15 µg/g H2O); (2) zinnwaldite granite quartz vary strongly in defect content and show the highest content of the dataset (10–70 µg/g H2O); (3) quartz from an underlying biotite granite have slightly lower, but very uniform contents down to the bottom of the borehole at 1600 m (average 20 µg/g H2O). Infrared spectra of Podlesí quartz reveal a gradual increase in total defect water content with increasing depth over 350 m (30–55 µg/g H2O). Lithium contents in quartz samples from the uppermost part of the Zinnwald intrusion correlate with the occurrence of Li-specific OH defects, while cathodoluminescence (CL) images do not show specific differences. Our findings evidence the potential of OH defects in quartz as a tool to decipher differentiation trends in igneous bodies, and the application of their eroded material for provenance analyses.