The use of zircon in the dating of geological processes and tectonic events has become a standard approach in many aspects of Earth science research. As a result, understanding how zircon interacts with aqueous fluids during metasomatism has become increasingly important. The alteration of natural zircon is driven primarily by coupled dissolution–reprecipitation or by ion-exchange with an aqueous fluid. In this study, whole and intact, euhedral light-brown zircon crystals (100–250 μm in length; 2 mg) from the Oligocene Fish Canyon Tuff (FCT) were experimentally reacted with an alkali-bearing reactive fluid and a REE + P source (0.5 mg CePO4 or 0.5 mg YPO4). Experiments were conducted in sealed Au metal capsules at 350 °C and 100 MPa for 182 days. During the experiment, the zircon became colorless, indicating annealing of the radiation damage in the crystal. Two-dimensional element maps of the outermost 3 μm of unpolished zircon crystal surfaces were produced using a grind of contiguous 7 μm analytical spots via laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS). The chemical maps indicate that the surface of the zircon crystals from each experiment heterogeneously reacted with the fluid, such that the Ce and Y concentration of chemically modified areas increased (by an order of magnitude) in the CePO4-bearing and YPO4-bearing experiments, respectively, when compared with the chemical maps of unaltered zircon grain surfaces. Helium ion microscopy of polished crystals revealed discontinuous micron-scale altered domains at the crystal margin, consistent with the findings of the unpolished mapping technique. Interestingly, the Th and U concentration of the altered zircon grain surfaces were consistent with the unaltered zircon regardless of the experiment. Incorporation of REEs on the zircon grain surface likely occurred via the coupled substitution REE3+ + P5+ ↔ Zr4+ + Si4+. The results from these experiments imply that the surfaces of minimally metamict zircon can be chemically modified by alkali-bearing fluids via ion exchange under lower greenschist pressures and temperatures over relatively short time periods with respect to the geological time scale.