Lignin, a naturally occurring biopolymer, is produced primarily as a waste product by the pulp and paper industries and burned to produce electricity. Lignin-based nano- and microcarriers found in plants are promising biodegradable drug delivery platforms. Here, we highlight a few characteristics of a potential antifungal nanocomposite consisting of carbon nanoparticles (C-NPs) with a defined size and shape containing lignin nanoparticles (L-NPs). Spectroscopic and microscopic studies verified that the lignin-loaded carbon nanoparticles (L-CNPs) were successfully prepared. Under in vitro and in vivo conditions, the antifungal activity of L-CNPs at various doses was effectively tested against a wild strain of F. verticillioides that causes maize stalk rot disease. In comparison to the commercial fungicide, Ridomil Gold SL (2%), L-CNPs introduced beneficial effects in the earliest stages of maize development (seed germination and radicle length). Additionally, L-CNP treatments promoted positive effects on maize seedlings, with a significant increment in the level of carotenoid, anthocyanin, and chlorophyll pigments for particular treatments. Finally, the soluble protein content displayed a favorable trend in response to particular dosages. Most importantly, treatments with L-CNPs at 100 and 500 mg/L significantly reduced stalk rot disease by 86% and 81%, respectively, compared to treatments with the chemical fungicide, which reduced the disease by 79%. These consequences are substantial considering the essential cellular function carried out by these special natural-based compounds. Finally, the intravenous L-CNPs treatments in both male and female mice that affected the clinical applications and toxicological assessments are explained. The results of this study suggest that L-CNPs are of high interest as biodegradable delivery vehicles and can be used to stimulate favorable biological responses in maize when administered in the recommended dosages, contributing to the idea of agro-nanotechnology by demonstrating their unique qualities as a cost-effective alternative compared to conventional commercial fungicides and environmentally benign nanopesticides for long-term plant protection.