Buffers containing high percentages of organic solvents, typically 50% of acetonitrile and/or methanol, together with sodium dodecyl sulfate (SDS) are employed for the separation and quantitation by electrokinetic chromatography (EKC) of analytes found in a nasal spray. Solutes consist of benzalkonium chloride, a family of highly positive compounds, and 2-phenylethanol and beclomethasone dipropionate, which are electrically neutral and poorly soluble in aqueous buffers. It is observed that the effect of both concentration of SDS and temperature on the separation depends on the organic solvent used and the solute nature. It is also observed that SDS-solute interaction for neutral and cationic compounds are weaker in the presence of high contents of acetonitrile than in methanol. Concentration of SDS, temperature, and organic solvent nature and content, allow one to modify the selectivity of the separation when neutral and ionic species have to be simultaneously determined. The optimization of EKC conditions enables the analysis of compounds in less than 5 min. A one-step sample treatment consisting of centrifugation of the nasal spray solved in acetonitrile, together with the referenced optimum separation conditions enable the reproducible quantitation of the analytes. Relative standard deviation values of inter-day migration times lower than 2.45% are obtained (R.S.D.n = 12), while R.S.D.n = 12 values for inter-day peak areas were lower than 6.32%.