Defined conditions of EOF along with different pH values of the BGE were compared for the purpose of analyzing glycopetides by CZE coupled to MS (CZE-MS). Hyphenation to MS involved ESI as well as MALDI, and single-stage and multistage MS were applied. Variation of the EOF was accomplished by selecting appropriate coatings for the capillary, namely hexadimethrine bromide (HDMB) and HDMB/dextran sulfate. A high and reproducible anodic and cathodic EOF, respectively, was obtained in both approaches, allowing the detection of analytes with net positive as well as negative charge in one single run. Thus, a fast and sensitive determination of the glycopeptides in a tryptic digest of antithrombin, chosen as a test sample, was achieved. Ionization suppression effects, a phenomenon typically observed with glycopeptides in MS analysis, were minimized thanks to separation from other peptides present. The high stability of the coatings permitted the generation of mass spectra without interfering peaks originating from the coating polymers. The high EOF generated by the coatings facilitated the maintenance of a stable spray when coupling to ESI-MS, and a stable CZE current when working with a sheath flow-assisted analyte deposition onto MALDI targets, respectively. In conclusion, CZE-MS could be demonstrated as a robust complementary method to capillary RP-HPLC-MS in combination with both soft-ionization techniques, ESI and MALDI, generally, and particularly in the context of glycopeptide analysis.