Zircon textures, chemistry and microstructures have been characterized in situ within Carboniferous sandstones from the Midland Valley of Scotland using back-scattered electron and cathodoluminescence images, electron backscatter diffraction techniques and chemical analyses. The study of polished thin sections reveals a variety of zircon types including unmodified detrital zircon, zircon outgrowths and different forms of modified zircon that formed in low-temperature conditions within the sedimentary rocks. These rocks have only experienced temperatures of <100 °C during burial; however, altered zircon is abundant and characterized by a low mean atomic number, with relatively high contents of non-formula elements and a nano-crystalline or microcrystalline structure. It forms by replacement of detrital zircon that subsequently became metamict. Two types of replacement mechanisms are effective in sedimentary environments and involve either dissolution–reprecipitation or solid-state reaction, but both require fluid access to the radiation-damaged areas. The former process appears to become the dominant replacement mechanism as temperature increases and produces highly porous, inclusion-rich zircon. Metamict zircon is extremely reactive in near-surface conditions and the production of low-temperature zircon is sensitive to both parent zircon characteristics and environmental conditions. As such, the alteration of zircon has the potential to yield unique information on the diagenetic history of sedimentary rocks. Low-temperature zircon would be unlikely to survive sedimentary transport or the rock crushing procedures that characterize many investigations of detrital zircon populations and consequently may generate severe biases in studies of this type.