The purpose of this study was to investigate the impact of emulsifiers and formulations on stratum corneum (SC) lipid conformation and evaluate confocal Raman microspectroscopy (CRM) as an alternative method to differential scanning calorimetry (DSC) in this research context. To this end, four different formulations were used: three conventional creams that contained ionic and/or non-ionic emulsifiers and one surfactants-free emulsion stabilized by a polymeric emulsifier. Additionally, all emulsifiers were tested in aqueous solutions/dispersions in the respective concentrations as present in the formulations. In this study, emulsifiers and formulations were applied onto excised porcine skin during incubation in Franz diffusion cells. Subsequently, SC was isolated, dried and subjected to CRM and DSC measurement to analyse lipid structural changes after treatment. In CRM measurement, 1080 cm−1/(1130 cm−1 + 1070 cm−1) peak ratio, which represents the C-C skeleton vibration and trans-gauche conformation order of lipids, was investigated. Various emulsifiers and formulations showed different impact on SC lipid conformation. Specifically, cetearyl alcohol and sodium cetearyl sulfate mixture dispersion showed the strongest ability among all studied emulsifiers, followed by glycerol monostearate, polyoxyethylene-20-glycerol monostearate as well as their mixture. Polysorbate 60, cetyl stearyl alcohol and their mixture did not affect SC lipid structure. The results of CRM and DSC correlated very well, indicating CRM, as an alternative to DSC, can be a reliable method to investigate SC lipid conformation.