Abundances of minor and trace elements in olivine are increasingly used as petrogenetic indicators for mantle source lithologies, mantle metasomatism history, mantle potential temperatures, and magmatic differentiation. As it is common for olivine to be complexly zoned on a fine-scale, high precision analytical methods for EPMA (electron microprobe microanalyzer, or Electron Microprobe) trace element analysis under high spatial resolution have been developed. However, previous studies have focused more on analytical precision with fewer efforts in examining the accuracy of the data. In this study, we used the Cameca SXFive field emission (FE) EPMA to fully evaluate the effects of beam settings, background offsets and background regression models, and primary calibration standards on the data accuracy of 10 key petrogenetic elements (Na, Al, P, Ca, Ti, Cr, Mn, Co, Ni, and Zn) using MongOlSh11–2 olivine as a reference material. Our results indicate that high voltage, high beam current and long counting time not only improve data precision, but also improve data accuracy, especially on elements with low P/B (peak/background) ratios such as Zn and Cr. Importantly, careful background offsets and background regression models need to be obtained via high resolution WDS relative scans or step scans on each target element. Special care needs to be paid to Co element analysis to avoid or correct for peak interference of Fe Kβ. Among 10 minor and trace elements, exponential background regression models need to be applied to Al, Mn, and Ti elements, whereas other elements require linear background regression. Furthermore, to avoid Al and Zn surface contamination due to alumina polishing or brass presence, ultrasonic cleaning between each intermediate polishing steps and plasma cleaning immediately prior to EPMA experiments is highly recommended. Micro-inclusions such as chromite and spinel in olivine or adjacent Ca-rich phases need to be avoided to minimize primary or secondary fluorescence-related contamination on Al, Cr, or Ca. As a volatile element, Na element needs to be analyzed first with appropriate counting time to minimize the Na loss under high beam conditions. It needs mentioning that major elements (Mg, Fe, and Si) are best analyzed using MongOlSh11–2 or San Carlos olivine as primary standards for calibrations, which can yield more accurate data for both major elements and trace elements because of the improved matrix-corrections. Using our recommended analytical protocols, we have successfully discriminated “depleted” mantle olivine cores from an EMORB in northern East Pacific Rise (EPR) via Ca, Ti, Ni, Co, and Mn abundances. Our olivine data from Siqueiros Transform and the nearby 8°20′ N seamounts also help reveal a metasomatized peridotite mantle beneath the northern EPR. Overall, the protocols proposed in this study can serve as a guide for accurate EPMA olivine trace element analyses, which potentially contributes to the efforts of fostering a comparable olivine database worldwide.