This chapter investigates the complex interactions between carbon-based nanomaterials (CBNs) and soil microbiomes, stressing their importance for soil health and ecosystem sustainability. Initially, an explanation of CBNs, including graphene, carbon nanotubes, fullerenes, and carbon nanoparticles, is offered, emphasizing their varied features and uses. The conversation then moves to the critical behavior of CBNs in soil environments. The chapter looks deeper into the mechanisms of interaction between CBNs and soil microbiomes, including adsorption to soil particles and microbe absorption, to better understand their effects on microbial diversity and community dynamics. Furthermore, the effects of CBNs on microbial activities, such as enzyme functions and nutrient cycling processes, are explored, as well as their impact on plant–microbe interactions and ecological ramifications. The environmental fate, transport, and possible risks associated with CBNs in soil ecosystems are also discussed, followed by mitigation techniques and future prospects for sustainable usage. This comprehensive study emphasizes the importance of a detailed understanding of CBN and soil interactions in order to determine policy and assure environmental safety.