In this data article, we provide information on the recovery rate and scanning electron microscope (SEM) images of the external morphology of zircon grains separated from two rock samples (AS3 and TEMORA 2) using both mechanical and electrical pulverization systems. The data in this article are related to the research article entitled "New insight into disturbance of U-Pb and trace-element systems in hydrothermally altered zircon via SHRIMP analyses of zircon from the Duluth Gabbro" (Takehara et al., 2018) [1]. Zircons from these two rock samples are widely used as reference materials for U-Pb dating by micro-beam techniques. Rock samples with nearly equal weights were pulverized by both methods, and the recovered zircon grains were then concentrated using conventional mineral-separation methods. Weights of the products at each step in the mineral separation process were measured, and finally the recovery rates of the heavy and non-magnetic minerals, including zircon, were calculated.