Soil is one of the dynamic components of terrestrial ecosystems and a critical basis for food security and ecosystem services. Sustainable management practices, based on integration of holistic and novel approaches of conservation tillage, cropping diversity with cover crops, and soil amendments can help to recover, maintain, and develop SQ to address food security challenges. Gypsum has long been used as one of the chemical amendments to improve crop yields and soil and water quality. The objectives of our study were to evaluate the impact of FGD-gypsum and cover crop on soil depth distribution of biological, chemical, and physical properties under continuous NT, and demonstrate the applicability of computing techniques and statistics-based models for selecting SQ indicators.