• Functionalized graphene at 25 mg/L significantly increased the height and root length of Vicia faba seedlings.
• Treatment with functionalized graphene enhanced the richness and diversity of both bacterial and fungal communities in the rhizosphere soil.
• The abundance of nitrogen-cycling bacteria (Hydrogenophaga, Sphingomonas, Nitrosomonadaceae) was altered, and beneficial fungi (Clonostachys, Dimorphospora) increased while phosphorus-solubilizing Basilicum decreased.
• Soil pH, organic matter, and total phosphorus were the main factors driving changes in microbial community composition, ultimately promoting plant growth.