Agriculture and other land use practices have severely affected the quality of soils and food production systems in South Africa. In addition, these practices significantly contribute to greenhouse gas (GHG) emissions. Soil quality is generally associated with soil organic matter (SOM) along with elemental Carbon (C) and Nitrogen (N). Approximately 58% of South African soils contain <0.5% organic C, 38% contain 0.5–2% organic C, and 4% contain >2% organic C. The extensive aridity and lack of SOM content in South African soils cause them to lack resilience and have a delicate nature compared to soils in temperate regions. In a country where almost 60% of the land is degraded, and 91% is prone to desertification, farming practices require a revised framework for land management. The challenge of producing food on degraded land that is often water-scarce and particularly vulnerable to the effects of climate change is a threat to South Africa's food and nutritional security. Therefore, this review aims to equip farmers with knowledge and principles of innovative and sustainable alternatives such as regenerative agriculture that naturally and progressively improves soil quality/fertility and ecosystem health; and reduces GHG emissions through carbon sequestration. Quantitative studies in South Africa show that during 5–90 years of crop cultivation in the Free State province resulted in a 10–73% reduction in C and N relative to natural grasslands. Similar studies reported a 50% reduction in C after 50 years of cultivation on Hutton soil in Pretoria; and a 50% reduction in C after only 3.5 years of cultivation in the Free State. Considering that the world's food systems are responsible for more than a third of anthropogenic GHG emissions, we are convinced that the shifting trend toward regenerative agriculture is a sustainable climate-smart solution for global food production systems.