Zein, a corn‐derived protein, has a variety of applications ranging from drug delivery to tissue engineering and wound healing. This work aims to develop a biocompatible scaffold for dermal applications based on thermally annealed electrospun propolis‐loaded zein nanofibers. Pristine fibers' biocompatibility is determined in vitro. Next, propolis from Melipona quadrifasciata is added to the fibers at different concentrations (5% to 25%), and the scaffolds are studied. The physicochemical properties of zein/propolis precursor dispersions are evaluated and the results are correlated to the fibers' properties. Due to zein's and propolis' very favorable interactions, which are responsible for the increase in the dispersions surface tension, nanometric size ribbon‐like fibers ranging from 420 to 575 nm are obtained. The fiber's hydrophobicity is not dependent on propolis concentration and increases with the annealing procedure. Propolis inhibitory concentration (IC50) is determined as 61.78 µg mL−1. When loaded into fibers, propolis is gradually delivered to cells as Balb/3T3 fibroblasts and are able to adhere, grow, and interact with pristine and propolis‐loaded fibers, and cytotoxicity is not observed. Therefore, the zein–propolis nanofibers are considered biocompatible and safe. The results are promising and provide prospects for the development of wound‐healing nanofiber patches—one of propolis' main applications.