The Idiwhaa gneiss, part of the Acasta Gneiss Complex, Canada, is a key source of information concerning formation of continental crust on the early Earth. However, zircon crystals from this oldest dated felsic crust were affected by multiple stages of alteration and metamorphism, leading to difficulties in disentangling primary from secondary processes. These grains provide an opportunity to understand the alteration processes that affect ancient zircon crystals. Ion imaging reveals pervasive recrystallisation fronts extending inwards from the margins of grains. Ahead of these recrystallisation fronts, grain cores contain isolated pockets of amorphous, but concordant, 3.99 Ga zircon that evidently escaped post-magmatic modification of U and Pb. The transport of these elements, involving the decoupling of parent and daughter isotopes, is highly heterogeneous over space and time within metamict zircon, yet localised domains still retain primary age information. Our data indicate that metamictisation of zircon alone does not lead to radiogenic Pb loss, which requires interaction with fluid.