Soil is the medium for plant growth and the substrate for all biogeochemical and biogeophysical processes. Soil’s unique natural organization forms the foundation of any food–water–energy nexus system. It forms a habitat for billions of diverse micro, meso, and macrofauna and flora and is the basis of numerous ecosystem services essential to human well-being and nature conservancy. It moderates soil hydrological processes within the entire vadose zone: which is part of the earth between the soil surface and the phreatic zone. Soil structure also supports numerous ecosystem services including nutrient transformation and availability, water quality and renewability, denaturing and transport of pollutants, and groundwater table fluctuations. It also moderates the soil–water–plant-energy nexus with the replenishement of green-water supply (from precipitation) for plants and soil biota, which in turn enables the production of biomass as a source of food, feed, fiber, and biofuel feedstock. Indeed, soil is a very large reservoir for water and carbon with strong influences on local, regional, and global climate. Also, the energy factor is connected with the climate change through soil–water–food–energy nexus because of numerous interlinked pathways including gaseous emissions, energy and food production, and recycling of nutrients and water at regional, national, and global scales. Through provisioning of numerous ecosystem services, the soil–water–food–energy–climate nexus is interwoven with the ecosystem security and functioning of planet’s four ecospheres (i.e., atmosphere, hydrosphere, lithosphere, and the biosphere). Therefore, the health of soil, plants, animals, people, and ecosystems is one and indivisible. This interconnectivity is also the basis of the “4 per Thousand” initiative adopted by the COP21, the Climate Summit of 2015 in Paris, and “Adapting African Agriculture” (AAA) by COP22 in Morocco. Consequently, soil is not only a foundation for securing the natural resources: food, water and energy, but it is under desperate need to be integrated and appreciated in understanding the complex interconnectedness of any food, energy, water and soil system. Concentration and stock of soil organic carbon are the key soil properties that determine the physical, chemical, biological, and ecological properties and processes, and are major control of all nexuses described herein. This chapter presents a conceptual model and the role of soil as a naturally organized medium to protect global food, water, energy securities. Moreover, it elaborates on using soil as a basic nexus tool and proposes a paradigm shift in integrating soil and creating the food–energy–water–soil nexus.