The response of garnet and zircon to prograde amphibolite-facies metamorphism in late Proterozoic mica schists from the Scottish Highlands has been investigated. Spatial analysis of zircon populations using scanning electron microscopy was undertaken in Dalradian Schists that have undergone a sequence of prograde garnet growth and localised breakdown reactions involving coupled dissolution–reprecipitation. Fluid availability and matrix permeability strongly control this metamorphic response and different generations of garnet contain radically different populations of metamorphic micro-zircon and associated changes in the detrital zircon population. Micro-zircon abundance increases during garnet growth, whereas that of detrital zircon decreases. The mineralogy of the matrix influences zircon abundance in porphyroblast phases, where garnet overgrows a micaceous matrix zircon-rich garnet forms and where it overgrows a quartzofeldspathic matrix the result is zircon-poor garnet. Following garnet growth, micro-zircon abundance decreases at each stage of the prograde reaction history, with sillimanite-zone schists containing the lowest abundance, suggesting micro-zircons are texturally less stable at staurolite- and sillimanite-grade metamorphism. Micro-zircons are distributed evenly across host minerals in the matrix, with the exception of retrograde chlorite where micro-zircons are absent due to fluids removing Zr before new zircon can precipitate. There is an overall decrease in the mode of zircon at each stage of the reaction history, indicating that zircon is a highly reactive phase during amphibolite-facies metamorphism and is very sensitive to individual prograde and retrograde reactions.