Nanoparticles (NPs) have generated significant interest in various fields due to the unique properties that materials exhibit at the nanoscale. This study presents a comparative analysis of copper nanoparticles (Cu-NPs) and cobalt nanoparticles (Co-NPs) synthesized via conventional solvothermal and green hydrothermal synthesis using ethylene glycol and Medicago sativa extract, respectively. The conventional solvothermal synthesis showed higher efficiency for both Cu-NPs and Co-NPs with yields of 32.5% and 26.7%, respectively. Characterization through UV-visible spectroscopy (UV-vis), Fourier-transform infrared spectroscopy (FTIR) and atomic force microscopy (AFM) revealed that while solvothermal synthesis produced larger particles (76.5 nm for Cu-NPs, 86.8 nm for Co-NPs), the green hydrothermal method yielded smaller particles (53.8 nm for Cu-NPs, 67.7 nm for Co-NPs) with better control over particle size distribution and spherical morphology, showing minimal agglomeration. UV-vis confirmed metal oxide formation, while FTIR showed complex patterns in NPs (green hydrothermal), indicating plant extract compounds. Antifungal evaluation against Pseudocercospora fijiensis showed complete inhibition at 2000 ppm for both NP types, with no mycelial growth after 30 days. When integrated into chitosan, solvothermal NPs produced rougher surfaces, and scanning electron microscope (SEM) confirmed the presence of copper and cobalt in the nanocomposites. This study provides insights into the synthesis of nanoparticles using an environmentally friendly process and their microbiological applications for future use in organic agriculture.