<p>Facility cultivation systems provide protection for jujube <i>(Ziziphus jujuba</i>) against rain-induced fruit cracking during the maturation and regulate the fruit ripening process. Prolonged cultivation within these controlled environments may alter the soil microbial community structure, potentially detrimentally affecting plant growth and fruit quality. There is a lack of information regarding the arbuscular mycorrhizal fungi (AMF) and bacterial communities in orchards under facility conditions. This study compared the soil bacterial and AMF communities in jujube orchards under greenhouse and rain shelter conditions. Greenhouse cultivation significantly increased soil organic carbon (SOC), total nitrogen (TN), and electrical conductivity, while it decreased soil pH compared to rain shelters. These changes were associated with reduced α-diversity indices in both bacterial and AMF communities. Non-metric multidimensional scaling analysis demonstrated distinct differences between bacteria and AMF communities under the two cultivation types. The phyla Actinobacteria, Gemmatimonadetes, and Rokubacteria were identified as key contributors to the observed alterations in the bacterial community, while variations in the genus <i>Glomus</i> and <i>Paraglomus</i> were responsible for changes in the AMF communities between the two cultivation types. Redundancy analysis revealed that pH was the primary factor shaping microbial community structure across the two cultivation types. Using a Zi-Pi plot, we identified several keystone ASVs, which showed a positive correlation with pH, SOC, and TN. The findings highlight the significant impact of cultivation type on soil microbial community structure and function, which has important implications for optimizing cultivation practices and ensuring sustainable jujube production.</p>