The aim of this study was to encapsulate the occlusion bodies (OBs) of Spodoptera frugiperda nucleopolyhedrovirus (SfNPV) in Eudragit® S100 microparticles (MPs), considering this technique as a possible alternative to protect them from deleterious environmental conditions. The MPs were prepared by oil-in-oil emulsion (O/O) solvent evaporation method. Experimental conditions were established according to a previous multi-level experimental design involving the core/polymer ratio as independent variable. The effects of these parameters on particle size and process yield were investigated observing that polymer concentration had a significant effect on particle size. After adequate conditions for MPs formation were determined, virus was encapsulated. The virus microparticles presented a particle size between 50–300 µm and concentration was 2.62 × 109 OBs g−1. Microencapsulation efficiency was 53.43% and virus release adjusted to Higuchi model suggesting diffusion as the release mechanism. Evaluated microencapsulation process protected viral particles of UV-inactivation, suggesting its potential for a biopesticide development.