Conservation agriculture practices, such as reduced tillage, cover crops and fertilization, are often associated with greater microbial biomass and activity that are linked to improvements in soil quality. This study characterized the impact of long term (31 years) tillage (till and no-till), cover crops ( Hairy vetch- Vicia villosa and winter wheat- Triticum aestivum, and a no cover control), and N-rates (0, 34, 67 and 101 kg N ha 1) on soil microbial community structure, activity and resultant soil quality calculated using the soil management assessment framework (SMAF) scoring index under continuous cotton