Frequent and severe droughts and reduced irrigation water availability in recent years have impacted soil health, soil organic carbon (SOC) storage, and nutrients in arid and semi-arid regions across the world. However, the magnitude and mechanisms of the changes in SOC and nitrogen (N) components and microbial community responses in lands experiencing irrigation retirement remain largely unexplored. We examined selected SOC and N pools and microbial community responses to diverse management strategies in silage corn (Zea mays) production under irrigation and after irrigation retirement in a clay loam semi-arid soil in New Mexico, USA. Under irrigation, mixed (CCM: grass, brassica, legume) and grass-only (CCG) cover crops with residue retained and mixed cover crops with residue removed (CCM-Rem) were examined. Under irrigation retired plots, perennial grass (PG) replaced CCG. Cover crops stored 13-19 % more SOC than fallow with no cover crop (NCC) in irrigated conditions, with up to 17 %, 59 %, and 41 % mineral-associated organic C (MAOC), potentially mineralizable C (PMC), and microbial biomass C (MBC), respectively. In irrigation retired plots, SOC was 14-26 % greater under cover crops and PG than NCC, with up to 24 % more SOC and 28 % more MAOC. Irrigation retirement increased particulate organic C (POC) by 80 % above the irrigated condition, representing a large portion of partially decomposed materials on the soil surface. Despite short-term increases in SOC fractions, a shift in the microbial community along with increased labile SOC following irrigation retirement may not lead to long-term C storage if proper conservation practices are not adopted. Cover cropping and PG enhanced the abundance of Actinobacteriota and Ascomycota, plant-associated microbes, while lowering the abundance of Chloroflexi. The Ascomycota, Mortierellomycota, and Bacteroidetes are linked to SOC storage due to their ability to rapidly accumulate microbial biomass. Cover crops and perennial grasses are crucial for preserving soil biological health and SOC storage in lands undergoing irrigation retirement.