Biopolymeric Chitosan-Carrageenan nanocomposites 66.6–231.82 nm in size containing the chemical fungicide mancozeb (nano CSCRG-M) were synthesized following a green chemistry approach. The physicochemical study of nanoparticles (NPs) was accomplished using a particle size analyzer, SEM and FTIR. TEM exhibited clover leaf-shaped nanoparticles (248.23 nm) with mancozeb on the inside and entrapped outside. Differential scanning calorimetry and TGA thermogravimetry exhibited the thermal behaviour of the nanoform. Nano CSCRG-1.5 at 1.5 ppm exhibited 83.1% inhibition against Alternaria solani in an in vitro study and performed as well as mancozeb (84.6%). Complete inhibition was exhibited in Sclerotinia sclerotiorum at 1.0 and 1.5 ppm with the nanoformulation. The in vivo disease control efficacy of mancozeb-loaded nanoparticles against A. solani in pathogenized plants was found to be relatively higher (79.4 ± 1.7) than that of commercial fungicide (76 ± 1.1%) in pot conditions. Nanomancozeb showed superior efficacy for plant growth parameters, such as germination percentage, root–shoot ratio and dry biomass. The nanoformulation showed higher cell viability compared to mancozeb in Vero cell cultures at 0.25 and 0.50 mg/mL in the resazurin assay. CSCRG-0.5 showed slow-release behavior up to 10 h. Thus, these green nano-based approaches may help combat soil and water pollution caused by harmful chemical pesticides.