We herein report a significant increase in sink strength and disease resistance in maize crop using copper-salicylic acid co-encapsulated chitosan nanofertilizer in seed treatment and foliar application. These chitosan nanofertilizer (0.01–0.16%) exhibited significant antifungal activity against post-flowering stalk rot (PFSR) in pot house [45.2–73.5% (mycelia growth) and 40.0–79.6% (spore germination)]. In field conditions, chitosan nanofertilizer (0.01–0.16%) effectively controlled the PFSR disease with PEDC (percentage efficacy of disease control) values of 68.6–93.8%. The results are evident with the significant improvement in defence enzyme activities namely phenylalanine ammonia lyase (PAL, 4.9 fold increase) and polyphenol oxidase (PPO, 2.3 fold increase). Crop growth parameters namely plant height, ear height, cob weight, test weight, grain yield/plot and biomass were also significantly improved. The grain yield increased by 1.8 fold proving that up-regulated source activity is coupled with elevated sink strength. Overall, we claim that the developed chitosan nanofertilizer serves both as a fertilizer as well as a pesticide. The developed fertilizer has agricultural importance and could be tested for its potential use in other crops.