In this work copper nanoparticles (Cu NPs) were prepared by using biopolymers soluble starch and sodium alginate (NaAlg) with its abundance of hydroxyl groups and its biocompatibility as the capping agents. Soluble starch capped Cu NPs (CuS NPs) and sodium alginate capped Cu NPs (CuA NPs) were first prepared by microwave assisted chemical reduction method using hydrazine, copper sulfate, soluble starch and sodium alginate as the reduction, oxidation and capping agents, respectively. The synthesized nanoparticles were characterized by x-ray diffraction (XRD), scanning electron microscopy (SEM), dynamic light scattering analysis (DLS), thermogravimetric analysis (TGA). The antifungal activities of the Cu NPs against Candida albicans and Candida krusei were determined depending on the stabilizing agents. The results showed that CuS NPs have better antifungal activity and stability under the open environment atmosphere than CuA NPs. For this reason, CuS NPs are thought to have the potential to be used in areas such as biotechnology and food packaging.