This study aimed to investigate different types of morphologies obtained using the electrospinning process to produce a material that enables wound healing while performing a controlled release. Using benign solvents, the authors prepared and characterised electrospun polycaprolactone mats loaded with propolis, a popular extract in traditional medicine with potential for skin repair. Different morphologies were obtained from distinct storage periods of the solution before electrospinning to investigate the effect of PCL hydrolysis (average diameters of fibres and beads: 159.2–280.5 nm and 1.9–5.6 μm, respectively). Phytochemical and FTIR analyses of the extract confirmed propolis composition. GPC and viscosity analyses showed a decrease in polymer molecular weight over the storage period (about a 70% reduction over 14 days) and confirmed that it was responsible for the nanostructure diversity. Moreover, propolis acted as a lubricant agent, affecting the spun solutions’ viscosity and the thermal properties and hydrophilicity of the mats. All samples were within the value range of the water vapour transpiration rate of the commercial products (1263.08 to 2179.84 g/m2.day). Even though the presence of beads did not affect the propolis release pattern, an in vitro wound-healing assay showed that propolis-loaded mats composed of beaded fibres increased the cell migration process. Thus, these films could present the potential for use in wound dressing applications.