Nanotechnology offers promising applications in agriculture, aiming to increase crop production while reducing environmental impact. Nanocarriers (NCs) enable the efficient transport of biologically active molecules, minimizing the required amount of bioactive compounds and allowing for controlled release over time. Recently, NCs have been proposed as a key technology for applying agrochemicals via unmanned aerial vehicles (UAVs). This study presents the results of using chitosan-based NCs to deliver and release natural compounds in a controlled manner, specifically extracts of Rubia tinctorum and Uncaria tomentosa, for the effective and sustainable control of phytopathogens in horticultural crops. The efficacy of NC-based treatments was demonstrated in vitro and ex situ against horticultural pathogens Botrytis cinerea, Cercospora beticola, Rhizoctonia solani, and Sclerotinia sclerotiorum. Mycelial growth inhibition values ranged from 187.5 to 375 µg/mL for NCs loaded with R. tinctorum extracts and 187.5‒500 µg/mL for those with U. tomentosa extracts. Complete plant protection of artificially inoculated sugar beet and carrot plants was achieved at doses ranging from 187.5 to 500 µg/mL, depending on the pathogen. Field tests conducted on sugar beet during the 2024 growing season yielded promising results for Cercospora beticola control. The absence of phytotoxicity and clogging problems during spray application represents a significant step towards optimizing the UAV field application of these treatments.