A green, simple, and cost-effective synthesis for copper nanoparticles has been investigated using ascorbic acid as a reductant and Citrus grandis peel extract as a stabilizer by microwave irradiation. In this method, using the pectin-enriched extract of Citrus grandis peel as a stabilizer for forming copper nanoparticles was potentially a new path for efficiently utilizing by-products. The effect of precursor, reductant, and stabilizer on the formation of copper nanoparticles by microwave irradiation and conventional heating was investigated. The obtained results indicated that copper nanoparticles were formed with a high-pure phase at an absorption maximum of 608 nm. Pectin-stabilized copper nanoparticles have a spherical shape with an average diameter of copper nanoparticles by conventional heating at approximately 9 nm and copper nanoparticles irradiated by microwave around 14 nm. The synthesized materials exhibited effective activity toward fungi with the IC₅₀ value of 2.59 and 3.28 pM for conventional heating and 3.03 and 2.69 pM for microwave irradiation against Fusarium solani and Colletotrichum gloeosporioides, respectively. Although the particle size and antifungal efficiency of copper nanoparticles synthesized by microwave irradiation and conventional heating seem similar, the shortened reduction, high-purity product, and high synthesis efficiency were considered outstanding advantages of microwave irradiation. Therefore, the synthesized copper nanoparticles using the mixture of extract of Citrus grandis peel and ascorbic acid under microwave irradiation was proposed as a promising method with eco-friendly and effective antifungal properties that can replace pesticides in crop production.