CE methods are valuable tools for medicinal plant quality management, screening, and analysis. Therefore, the aim of the current study was to optimize and validate a CE-MEKC method for simultaneous quantification of four chief bioactive metabolites from Plantago species. The two most important secondary metabolite groups were aimed to be separated. Different electrolyte and surfactant types were tested. Surfactant concentration, BGE pH, electrolyte concentration, and buffering capacity were optimized. The final BGE consisted of 15 mM sodium tetraborate, 20 mM TAPS, and 250 mM DOC at pH 8.50. Acceptable precision, good stability, and accuracy were achieved, with high resolution for phenylethanoid glycosides. Analytes were separated within 20 min. The method was shown to be suitable for the quantification of the iridoid glycosides aucubin and catalpol, and the phenylethanoid glycosides acteoside (verbascoside) and plantamajoside from water extracts of different samples. The method was shown to be applicable to leaf extracts of Plantago lanceolata, Plantago major, and Plantago asiatica, the main species with therapeutic applications, and a biotechnological product, plant tissue cultures (calli) of P. lanceolata. Baseline separation of the main constituents from minor peaks was achieved, regardless of the matrix type.