In situ isotopic (U-Pb, Lu-Hf) and trace element analyses of zircon populations in six samples of the intrusive Mawson Charnockite, east Antarctica, emphasise complex zircon behaviour during very high-grade metamorphism. The combination of geochemical data sets is used to distinguish xenocrysts and identify a population of primary igneous zircon in situations where U-Pb data spread close to concordia over a few hundred Myr. The population is filtered to exclude grains with: (1) U-Pb ages > 2% discordant, (2) anomalous trace element-content (Th, U, Y, REE) and (3) outlying Hf-isotopic values. Rare metamorphic-type grains were also excluded. Upon filtering the population, minimum emplacement ages for each sample were determined using the oldest grain(s). This approach improves upon age determinations in complex data sets that use weighted mean or isochron methods. Our results suggest that the Mawson Charnockite was emplaced episodically at c. 1145-1140 Ma, c. 1080-1050 Ma and c. 985-960 Ma. Core-outer core-rim and core-rim textures were identified but are not correlated with U-Pb ages. We establish that recrystallisation (mainly of zircon rims) must have occurred shortly following igneous crystallisation and that metamictisation/cracking is a Paleozoic to Recent event. Therefore, intra-zircon diffusion in a high-T, high-strain environment during Meso-Neoproterozoic orogenesis is inferred to have caused the extensive U-Pb isotopic disturbance. Charnockitic magmatism prior to c. 1,000 Ma has not previously been recorded in the Mawson region and indicates that orogenesis may have commenced c. 150 Myr earlier than previously thought. Correlations with similar aged rocks in adjacent regions have implications for supercontinent reconstructions.