In this work, we investigate whether microemulsions may be employed as delivery systems of AMPs. Specifically, we investigate (i) structural parameters of microemulsions believed to affect skin permeation, e.g. through tight junctions in the stratum corneum, and (ii) interactions between hydrophobic and hydrophilic AMPs and microemulsions. Results from SAXS measurements are combined with data from cryo-TEM, skin permeation studies, and bacterial killing assays. In doing so, we aim at elucidating whether AMPs affect microemulsion structure, and how this may depend on properties of both microemulsion and AMP, and subsequently if structural parameters can be associated with skin permeation and antimicrobial effects in the skin.