Zircon, with a chemical formula of ZrSiO4, is a widely used mineral for determining the crystallization age of igneous rocks. It is also used to constrain the timing of metamorphic events from its overgrowth or recrystallized domains. Furthermore, detrital zircon grains can provide information on the sedimentary provenance. Due to the trace amounts of uranium (parent) which decays into its daughter element (Pb), it is a prime geochronometer for the majority of magmatic and metamorphic rocks. With high-precision analytical instruments, such as TIMS, SIMS, and LA-ICP-MS, huge amounts of geochronological and trace element data from zircon have been generated around the globe to date. Target domains within zircon grains are analyzed to extract geochemical and geochronological records using spatially resolved techniques such as ion probes or laser ablation coupled with mass spectrometry. Before any such analysis, the zircon grains are examined for internal structures, growth zoning, and the presence of tiny inclusions. However, many researchers analyze multiple domains within single zircon grains for U-Pb isotope analysis with little regard for their internal structures, particularly crystallographic orientations. Hence, they may obtain mixed ages with variable discordance, leading to imprecise interpretation especially when the growth domains are not well-identified. Particularly, zircon grains that contain multi-growth domains or have local internal deformations within a single grain may not produce geologically meaningful age results if the analyses are conducted on mixed domains. This study presents a brief review on zircon geochronology, how to identify and visualize micro-deformations in metamorphic zircons through the EBSD analysis, and the effects of micro-deformation on age results. Examples from a case study conducted on zircons hosted in the Himalayan high-pressure eclogites are presented that show intra-grain plastically deformed domains and their effects on the corresponding age results.