The preservation of original water contents within nominally anhydrous minerals is essential for understanding the deep Earth’s water budget. Here we present a comprehensive analysis of mineral chemistry and Fourier transform infrared spectroscopy on 15 lower-crustal granulite xenoliths collected from Damaping in the North China craton. Our analyses reveal that the orthopyroxene grains from two samples exhibit hydrogen-deficient rims, suggestive of hydrogen loss. Drawing upon experimentally determined hydrogen diffusivity in pyroxene, we propose that clinopyroxene, despite the absence of evident hydrogen zoning, may have likewise undergone partial hydrogen depletion. Our findings call into question the conventional belief that hydrogen concentrations in pyroxene are faithful proxies for the original water content in the continental lower crust. We attribute the loss of hydrogen in pyroxene to magmatic outgassing, most likely occurring during the surface flow stage. Such a process could partially explain the relatively lower water contents documented in the granulite xenoliths when compared to those found in the Precambrian granulite terranes from the North China craton. Considering recent studies on mantle xenoliths, it becomes evident that both basalt-hosted mantle and lower-crustal xenoliths may have experienced partial loss of their original water contents within the deep Earth.