The trace elements in quartz, Al and Ti, contain considerable information about mineral genesis, and determining their concentrations is of great importance in geology. Electron probe microanalysis has the advantages of non-destructive testing and high spatial resolution; however, it is a challenge to improve the accuracy and precision of trace element detection using this method. The important factors affecting accuracy include the fragility of quartz lattices at high beam currents and the methods used to determine the background. In this paper, the peaks of Al-Kα and Ti-Kα, and their backgrounds, were found to exhibit intensity variations at high beam currents and small beam diameters; therefore, it is necessary to select a large beam diameter (up to 20 µm) to avoid variations in intensity at high currents (500 nA). For background determination of Al, a multipoint background method is proposed to determine the background value, which greatly improves the accuracy of the results. For Ti, the choice of background measurement does not affect the result. In addition, it is verified that the background obtained from other quartz samples can be used as the background of an unknown quartz sample, which reduces the analysis time and minimizes sample damage.