Botrytis cinerea, the primary cause of gray mold in vineyards, significantly impacts the wine industry by reducing both yield and quality. While chemical fungicides remain the primary control method, their use has led to pathogen resistance and raised concerns about toxicity to human health and the environment. The demand for zero-residue wines necessitates alternative approaches. Natural bioactive products (NBPs) offer a promising solution by inhibiting pathogen growth and reproduction. However, their field application is challenging due to instability, solubility issues, and lack of specificity. Nanoencapsulation can enhance NBP efficacy, but the development and application of nanocarriers (NCs) require a multidisciplinary approach to overcome scientific and technical hurdles. This study presents the results of in vitro, ex-situ, and field application tests against B. cinerea using Rubia tinctorum and Uncaria tomentosa extracts encapsulated in chitosan-based NCs. Laboratory tests revealed high efficacies, with minimum inhibitory concentrations (MICs) of 250‒375 μg/mL in range and complete protection of artificially inoculated 'Tempranillo' grapes at MIC doses. Field trials conducted in a D.O. Ribera de Duero vineyard during the 2024 growing season showed promising results, with no signs of phytotoxicity and no adverse effects on grape must quality parameters. These findings suggest that biopolymeric NCs offer a non-toxic and eco-friendly platform for delivering NBPs without compromising wine quality.