Vaccines provide great benefit for global health, but are insufficiently distributed in developing countries due to high costs of manufacturing and limited storage stability. Spray drying formulations of peptide-based vaccines offer a promising strategy to reduce production costs and improve unrefrigerated storage stability. This design of experiments investigated how adjusting spray drying parameters (inlet temperature, atomization pressure, feed rate and aspiration rate) affects residual moisture and reconstitution properties of the powder product, and morphology and size of the rehydrated particles. An emulsion capable of forming cubosomes with the protein ovalbumin as model antigen was used as vaccine formulation and spray dried. The produced powders had low residual moisture content, independent of the spray drying parameters within the range investigated. Cryogenic transmission electron microscopy revealed that cubosomes were produced after rehydration regardless of the spray drying parameters. Furthermore, dynamic light scattering showed that the average diameter of the rehydrated particles consistently was close to 230 nm at any combination of spray drying parameters as long as the outlet temperature was kept below a threshold of 115 °C. The process thus appears to be robust allowing optimization to be focused on yield, dry particle engineering or outlet temperature considerations.