Healthy and productive soils are fundamental for the provision of essential ecosystem services that underpin food security and improved nutrition, climate change adaptation and mitigation, and sustainable development. A new paradigm and the re-designing of the agricultural systems based on healthy soil is essential for development of a more sustainable agriculture and a greener eco-environment and food industry in the future. As brought into focus by the World Soil Day 2020 motto, “Keep soil alive, protect soil biodiversity”, soil ecological engineering is one solution which aims at maximizing soil biodiversity-driven ecosystem delivery in cropping systems while reducing the excessive reliance on agrochemicals. More importantly, system and holistic approaches capturing the interactions of the climate, soil, crops and management are indispensable for producing healthy food and achieving the goals of agricultural green development.