Oscillatory zoning — alternating high- and low-impurity (trace element) zones — is a hallmark of magmatic zircon from felsic systems and preserves the history of magmatic systems. Although commonly attributed to fluctuations in temperature, pressure, or melt composition, the mechanisms driving this zoning remain uncertain. Here, we show that high-impurity growth zones, which appear homogeneous when imaged with a scanning electron microscope (SEM), actually consist of finer-scale growth zones when viewed at the nanoscale - and still finer zones are revealed at the atomic scale. The apparent homogeneity in SEM images results from electron beam convolution, where features smaller than the beam’s interaction volume cannot be resolved. Backscattered electron images have higher spatial resolution than cathodoluminescent images, but high-impurity zones imaged with both are found to consist of finer zones at the atomic scale when imaged with atom probe tomography. Adjacent low-impurity zones are homogeneous across all scales. We interpret these observations as evidence of impurity poisoning during near-equilibrium zircon growth. Faceted crystal growth at low supersaturation leads to rejection of impurities, except for those allowed by equilibrium partitioning. Rejected impurities accumulate on the crystal surface, blocking normal incorporation of atoms and temporarily halting growth. When supersaturation exceeds a critical threshold, growth resumes, trapping the adsorbed impurities and forming a high-impurity zone. These findings not only help to resolve the origin of oscillatory zoning in zircon but also establish a generalizable mechanism of impurity poisoning during near-equilibrium crystal growth, redefining how mineral records are interpreted in igneous systems and beyond.