Intracytoplasmic sperm injection (ICSI) is the only method for in vitro embryo production (IVP) in horses. Besides oocyte developmental competence, the outcome of IVP is also highly dependent on sperm quality. Therefore, it is not only essential to employ superior methods of selecting high quality sperm, but also to be able to characterize which quantifiable properties of sperm quality are most indicative of its fertility. In men, a net negative surface charge, estimated by zeta potential (ZP) is highly correlated with sperm quality and in vitro embryo developmental outcomes. However, there is no information available about approximate charges or ZP in equine sperm. Therefore, in this study we aimed to characterize equine sperm ZP and identify its associations with known measures of sperm quality. Additionally, we aimed to complete a comprehensive comparison of conventional sperm selection techniques as compared to the novel method of microfluidic sorting. Ejaculates (n = 22) were partitioned into fresh (∼23 °C, 0 h; n = 12) and cooled (∼4 °C, 24 h; n = 10) groups, and processed by swim up (SU), density gradient centrifugation (DGC), density gradient-swim up combination (DG-SU), and microfluidic chip (MF) sorting. Motility, progressive motility, cell viability, normal morphology, and ZP were evaluated for both unprocessed fractions and post-selected fractions. The ZP of both fresh and cooled samples was net negative and also correlated with motility and progressive motility for both fresh and cooled samples (P < 0.05). The ZP of cooled samples was also correlated with viability (P < 0.05). Among the compared methods of sperm selection, MF was highly effective in selecting high quality sperm as determined by the measured parameters. Percent motility, progressive motility, normal morphology, and viability of MF selected sperm were of higher quality than sperm selected by SU, and of similar to DG-SU and DGC without the use of potentially harmful centrifugation steps. Correlations between ZP, motility, and viability parameters may indicate a role of external charge on the motility and survival of sperm within the female reproductive tract. In conclusion, we identified an average net negative ZP on equine sperm and correlations between ZP and other measures of sperm quality, as well as having identified MF as a novel effective method of equine sperm selection for IVP., Competing Interests: Declaration of competing interest All of the authors have agreed to the submission of this manuscript and to be responsible for its contents and declare no conflicts of interest., (Copyright © 2022 Elsevier Inc. All rights reserved.)