Soil microbial community structure and functioning, including substrate catalysis and nutrient cycling, in agroecosystems vary with soil management practices. Intensifying and diversifying cropping systems by integrating cover crops can increase microbial abundance and enzyme activities. The main objective of this study was to evaluate the response of different cover crops (single as well as in mixture) on soil bacterial and fungal communities, as well as potential enzyme activities associated with SOC dynamics and soil biogeochemical cycling, in a limited-irrigation winter wheat-sorghum-fallow system in the semiarid southern High Plains.