This study examines the influence of temperature, eluent modifier type and concentration, and mobile phase flow velocity on the separation efficiency of caffeine (CAF) and phenol (PH) in Hypersil GOLD HILIC and Shodex SILICA 5NH 4D chromatographic columns. A thermodynamic analysis demonstrated that the adsorption processes of these compounds are primarily exothermic and depending on the eluent type. Acetonitrile-water (ACN:H₂O) systems provided superior selectivity between caffeine and phenol compared to methanol-water (MeOH:H₂O) systems, with selectivity improving as temperature increased in ACN:H₂O systems. Variations in eluent modifier concentration significantly impacted retention times, suggesting diverse interaction mechanisms between the analyzed compounds and the stationary phase. Furthermore, studies on column efficiency indicated that faster eluent flow reduced separation efficiency, as evidenced by HETP values. The optimal flow rates were determined to range between 0.2 and 1.25 ml/min, depending on the column tested.