Agroforestry (AF) is a popular farming technique and a perfect scientific approach that can help to manage resources sustainably and reduce greenhouse gas (GHG) emissions. Using an agroforestry system (AFS) greatly increases Soil organic carbon (SOC), and in many cases, it also enhances farm diversity, microclimate, and many other factors. This happens as a result of adding suitable, deeply rooted multipurpose perennial crops to an AFS that efficiently cycles and pumps nutrients, restocking the soil. By using multidisciplinary research in AF, nanotechnology can improve crop, animal, and tree productivity in a sustainable manner. Additionally, it can help with crop post-harvest management, precise virus diagnosis, targeted pesticide delivery, and disease identification. The soil carbon (C) sequestration, tree-based nanomaterial biosynthesis, SOC, and numerous other ecological processes can also be aided by this nanotechnology-assisted AF. The production of green nanoparticles (NPs) namely iron (Fe) NPs, silver (Ag) NPs, and gold (Au) NPs from AF tree species such as Albizia adianthifolia, Emblica officianalis, Moringa oleifera, Tamarindus indica, and Terminalia chebula is becoming more significant. This can help with accessibility, dependability, safety, and sustainability issues that nanotechnology is currently facing. Through case studies, this chapter explores the benefits, challenges, and potential uses of nanotechnology in soil C sequestration in AF and other Land use systems (LUS). In addition to its notable effects on crop yield and soil characteristics, more studies can clear up doubts regarding NM's ability to tackle problems that modern-day AF faces, including problems with accuracy, volatility, phytotoxicity, and bioaccumulation.