Backgrounds and aims <p>Plant-associated arbuscular mycorrhizal fungi (AMF) participate in soil carbon storage. Due to multiple benefits of AMF to plant and soil health, AMF has gained much attention leading to an expanding market in mycorrhizal bio-stimulants for various crops, including citrus. However, there is limited information on how inoculation of a mature citrus orchard with AMF affects C storage and microbial community.</p> Methods <p>A field trial was conducted with three treatments applied in the alleyways: a cereal cover crop inoculated with AMF at seeding, a cover crop without inoculation, and a control. Soil C dynamics indicators including total soil C, permanganate oxidizable carbon, mineralizable carbon, and soil aggregation were assessed. Microbial community biomass was assessed with soil phospholipid fatty acids and neutral lipid fatty acids.</p> Results <p>After two years of treatment implementation, AMF inoculation had no significant effects on soil C dynamics indicators, but total soil C, Min C, and small macroaggregates were higher in the alleyways compared to the tree rows in the topsoil. After three years, AMF inoculation had no significant effect on microbial community biomass. Across treatments, alley rows supported higher microbial community biomass and had higher total soil C, POXC, and Min C than the tree rows.</p> Conclusion <p>To summarize, AMF inoculation may not be needed in soils with high native abundance, weeds can promote soil health, alley management effects extend beyond the cover crop strip, and AMF may have an indirect influence on soil C dynamics by promoting bacterial biomass.</p>