Good soil quality implies the maintenance of properties at levels capable of ensuring an equilibrated and healthy ecosystem, with sustained agricultural production to supply the world population. Climate change, land-use change, and agriculture intensification are causing a decline in soil quality, which in most parts of the world is becoming severe (desertification). Land-use changes, the associated loss of soil organic matter (SOM), and beneficial microbial diversity are major reasons for deteriorating soil fertility and declining agricultural productivity, as well as affecting water, air, and biodiversity. Adaptation towards climate-resilient and climate-smart agriculture is necessary to cope with climate change and extreme events. This requires the following measures: (1) sustainable production (integrated livestock and cropping systems, including agroforestry); (2) increased soil organic matter (SOM) (bio-based and organic fertilizers, crop rotations, crop associations, no-till, conservation agriculture, C sequestration, and microbial processes); (3) reduced greenhouse gas emissions, less nutrient losses from agriculture, and increased nutrient use efficiency (NUE) (precision agriculture).