An efficient bioprocess using immobilized lactic acid bacteria to obtain 5-iodouracil-2'-deoxyriboside, known as idoxuridine, is reported. This nucleoside analogue is an antiviral agent used in the treatment of viral infections in the absence of efficient vaccines. Idoxuridine conversion was close to 90% in different nonconventional media. A bionanocomposite (alginate-nanoclay) was employed as matrix to stabilize Lactobacillus animalis ATCC 35046 with improved stability in the presence of organic cosolvents. In this study, an eco-compatible and alternative bioprocess to obtain idoxuridine was developed for the first time. The scale-up biosynthesis of idoxuridine afforded a product yield close to 0.4 gr/L in the presence of 20% of DMSO.