The Um Ara granites are a suite of granitoid rocks located in the southern part of the Eastern Desert of Egypt. The integration of various electron probe micro analyzer (EPMA) techniques, such as backscattered electron (BSE) imaging, X-ray compositional mapping, and wavelength dispersive spectrometry (WDS), has provided valuable insights into the alteration process of zircon in the Um Ara granite. The zircon exhibits high concentrations of non-formula elements such as P, Al, Ca, Fe, Ti, and REEs, suggesting that the alteration involved coupled dissolution-reprecipitation processes influenced by aqueous fluids. The negative correlations between Zr and the non-formula elements indicate that these elements were incorporated into zircon at the expense of Zr and Si, significantly affecting the distribution and fractionation of REEs in the original zircon. Based on the presented data and literature knowledge, the sequence of alteration events is proposed as follows: (1) initial zircon crystallization around 603 Ma accompanied by the formation of other U- and Th-bearing minerals like xenotime, thorite, monazite, and apatite; (2) long-term metamictization leading to fractures and cracks that facilitated fluid circulation and chemical changes; (3) a major hydrothermal event around 20 Ma that released a suite of non-formula elements from the metamicted zircon and associated minerals, with the enriched hydrothermal fluids subsequently incorporating these elements into the modified zircon structure; and (4) further low-temperature alteration during subsequent pluvial periods (around 50,000–159,000 years ago), facilitated by the shear zones in the Um Ara granites, may have allowed further uptake of non-formula elements. The interplay between hydrothermal fluids, meteoric water, and the shear zone environments appears to have been a key driver for the uptake of non-formula elements into the altered zircon.