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Abstract Zircon in mudstones, sandstones and greenschist facies metasediments has been investigated using conventional SEM techniques (BSE, CL and SE imaging) and reveals highly variable microstructures and textures. In these rocks, zircon readily responds to low temperature events due to radiation damage in its crystal lattice while crystalline zircon remains unmodified. Zircon that alters as a result of metamictization has a low BSE intensity (dark BSE zircon) and electron microprobe measurements show an enrichment of Mg, Al, Ca, Fe, Y and a loss of Si and Zr, while Hf appears to remain relatively constant between the unmodified parent and the resulting modified phase. Dark BSE zircon forms via two main mechanisms. The dominant dark BSE zircon form (Group 1) has a microstructure containing an abundance of pores, cavities and inclusions forming as a result of a coupled dissolution-reprecipitation mechanism. Electron backscattered diffraction (EBSD) analyses suggests that the structure is composed of randomly orientated nanocrystalline zircon. The other form of dark BSE zircon (Group 2) is produced by a solid-state diffusion-driven cation-exchange process in which structural recovery occurs (as determined by EBSD) and where inclusions or pores are absent in the microstructure of the product phase. The different forms of altered zircon are chemically indistinct. Zircon outgrowths (c.1µm thick) on the margins of detrital unmodified zircon in clay-rich sandstones indicate Zr was transported from altered grains. These zircons crystallised below 100°C. The upper temperature at which metamict zircon may be dissolved is constrained by the annealing temperature of the zircon lattice whereby metamict areas are repaired above c.250°C. Zircon outgrowths are larger (c.3µm thick) and in much greater abundance in slates that have experienced deformation and temperatures c.350°C. They have a complex microstructure, partly as a result of interactions with xenotime that also forms outgrowths upto 12µm thick on zircon. Xenotime inclusions and zircon-xenotime complexes have been identified within zircon outgrowths using TEM and LV-STEM. Electron transparent foils of the outgrowth were prepared using the FIB microscope. Zircon outgrowths have similar chemical characteristics to dark BSE zircon but have distinctly different substitution relationships. There are also differences between the chemistry of dark BSE zircon from sedimentary and greenschist facies rocks where the latter is considerably more enriched in Al, Y and Ca. The implications of this are that zircon chemistry is strongly influenced by the local conditions in which in formed. Sedimentary processing causes considerable bias in the zircon population. Fine-grained sediment is a sink for high U and Th, heavily radiation damaged, old zircon in comparison to mature sediment that is likely to contain an abundance of low U and Th zircon or young zircon upon deposition. Small metamict zircon fragments are prone to dissolution and can be readily stripped from the matrix of fine-grained sediments. The concentration of zircon outgrowths in fine-grained sedimentary and metasedimentary rocks is primarily the result of sedimentological processes. The findings of this work illustrate the importance of studying minerals in-situ and within their petrological context. The wide-spread and abundant nature of low temperature zircon is a major consideration for geochronology, sedimentary provenance studies, the interpretation of zoning in zircon and has significant implications for the long-term storage of radioactive material.