Blueberry is a shallow root plant in which the absorption of nutrients is inefficient, resulting in slow growth under artificial cultivation conditions. Endophytes play an important role in promoting plant growth; however, the effects of Trichoderma spp. and dark septate endophytes (DSEs) on host plant growth and soil microorganisms are still debatable. We isolated two endophytic fungal species, Trichoderma koningiopsis (TK) and a DSE (Amesia nigricolor; AN), from blueberry roots, which can solubilize insoluble phosphorus and produce amylase and cellulase to promote plant growth. We found that under dual inoculation, the colonization rate and colonization intensity of TK were higher than they were under single inoculation with TK, while the colonization rate and colonization intensity of AN were lower under dual inoculation than under single inoculation with AN. The plant nutrients, root activity, available potassium, and parts of soil phosphatase activities were highest under dual inoculation. TK inoculation resulted in the highest diversity and richness in the soil fungi and bacteria, followed by dual inoculation. The abundance of Ascomycota, Acidobacteriae, Firmicutes, and Actinobacteriota increased significantly, resulting in Trichoderma and Vicinamibacteria inoculated with TK, Chaetomium and Alicyclobacillales inoculated with AN, and Hypocreales and Burkholderiaceae with dual inoculation enriched in the soil.