The biological control of SWD using entomopathogenic viruses offers a sustainable alternative to chemical insecticides; however, viral instability under environmental and digestive conditions limits their application. Here, we present a chitosan–TPP encapsulation system designed to protect and control the release of Drosophila C virus (DCV) and La Jolla virus (LJV). Physicochemical characterization by dynamic light scattering (DLS) and zeta potential measurements confirmed successful encapsulation and indicated that stable electrostatic complexes form within a narrow pH range where chitosan is positively charged and the virion surface is negatively charged. The encapsulated viruses remained intact under acidic conditions but were rapidly released under alkaline conditions mimicking the posterior midgut of SWD. Encapsulation efficiency increased with decreasing chitosan molecular weight and higher stirring speed, reaching up to 90%. Bioassays demonstrated that both formulated viruses caused high mortality in adult flies, with no adverse effects from the carrier matrix. These findings establish chitosan–TPP formulations as an effective strategy for virus stabilization and targeted release in biological pest control.