This work presents data for the mineral assemblages, composition and Raman spectroscopy of proximal secondary Be and associated minerals in pseudomorphs after beryl from granitic pegmatites located along the contacts of major regional geological units. The pegmatites differ in their position relative to the ductile to brittle shear zones within the Rožná-Olší ore field (U-deposit), Czech Republic. Extensive dissolution of beryl crystals in the beryl–columbite pegmatites Drahonín IV and Věžná I situated within or close to the shear zones is evident in contrast to minor alteration of beryl in the Dolní Rožínka and Kovářová pegmatites located outside of the shear zones. Near-total replacement of beryl crystals, up to 40 cm in length, from the Drahonín IV pegmatite, located in the Olší shear zone formed the following secondary Be minerals in order of their abundance: bavenite–bohseite > bertrandite ≫ milarite > hydroxylgugiaite. This assemblage is also characterised by the presence of sulfides (pyrite, galena, sphalerite) and zeolites. Such an extensive replacement process required a substantial fluid flow and is very possibly related to the pre-uranium quartz–sulfide and carbonate–sulfide mineralisation events within the Rožná-Olší ore field. Alteration products resulting from breakdown of beryl in the Věžná I pegmatite follow the sequential substages (bertrandite + K-feldspar ± harmotome → epididymite + K-feldspar → hydroxylgugiaite + K-feldspar) and locally show cross-cutting textures. These assemblages were generated by post-magmatic residual fluids (early assemblage bertrandite + K-feldspar) as well as fluids related to a retrograde stage of metamorphism, compositionally contrasting with the host serpentinite, and perhaps also hydrothermal processes associated with the Olší shear zone. The pegmatites Dolní Rožínka and Kovářová, located outside of the shear zones, exhibit only a low degree of alteration and have differing textural and paragenetic development. Highly variable assemblages of secondary minerals after beryl are excellent mineral indicators of hydrothermal overprinting in granitic pegmatites during a variety of subsolidus processes.