Recently, nanoemulsion-based gels have become very popular for dermal drug delivery, overcoming the disadvantages of conventional semi-solid drug forms. The aim of this study is to prepare and characterize nanoemulsion-based hydrogels and organogels containing combined propolis and dexpanthenol, and to compare their stability, antimicrobial, and cytotoxicity properties. Within the scope of characterization studies, organoleptic properties, drug content, morphology, pH, gel-sol conversion temperature, spreadability, viscosity, FT-IR, and release properties were evaluated in hydrogels and organogels. The characterization studies carried out were subjected to short-term stability evaluation at room temperature and refrigerator for 3 months. While no phase separation was observed in any of the formulations kept in the refrigerator, phase separation was observed in four formulations kept at room temperature. The release study successfully obtained an extended release for propolis and dexpanthenol. In the antimicrobial susceptibility study, Hydrogel 1 showed activity against S. aureus, while Organogel 1 showed activity against both S. aureus and S. epidermidis. In the cytotoxicity study against HDFa cells, both Hydrogel 1 and Organogel 1 were found to be nontoxic at low doses. These hydrogels and organogels, which contain propolis and dexpanthenol in combination for the first time, are promising systems that can be used in wound and burn models in the future.