The interaction of active substances with molecular structures in stratum corneum (SC) is crucial for the efficacy and safety of cosmetic formulations and topical drugs. However, the molecular architecture of SC is highly complex and methods to unambiguously localize exogenous molecules within SC are lacking. Consequently, little is known about the distribution of actives within SC, and proposed penetration mechanisms through SC are typically limited to simple diffusion via a tortuous (lipid only) or transverse (across corneocytes and lipid matrix) pathway. In this work, 3D mass spectrometry imaging is used to determine the spatial distributions of four active substances at subcellular resolution in SC, including partitioning between the corneocytes and the intercellular lipid matrix. The results indicate that caffeine, 2-methyl resorcinol and oxybenzone are homogeneously distributed in the corneocytes but largely absent in the lipid matrix, despite considerable differences in lipophilicity. In contrast, the distribution- of jasmonic acid derivative is more inhomogeneous and indicates considerable localization to both the lipid phase and the corneocytes.