Aims <p>Organic fertilizers can improve plant growth, resistance, soil properties and microbial diversity. However, few research has focused on the effects of organic fertilizers on apple plant growth under drought stress (DS).</p> Methods <p>In this study, by determining plant growth-, soil physicochemical property-related parameters and analyzing soil microbial community diversity and composition, we explored the effects of manure organic fertilizer (MOF) and weathered coal organic fertilizer (WOF) on apple plant growth, soil fertility and microbial community under DS.</p> Results <p>Both MOF and WOF applications improved apple growth and drought resistance (with WOF having a more pronounced effect), and enhanced soil fertility and enzyme activities (with MOF having a more pronounced beneficial effect). Under well-watered condition (WW), MOF and WOF decreased bacterial diversity but increased fungal diversity, with effects reversed under DS. Under WW, both fertilizers significantly increased Proteobacteria abundance while reduced Actinobacteria abundance. Under DS, MOF increased Bacteroidota and Ascomycota abundance, and WOF increased Actinobacteria abundance. Mantel’s test and RDA indicated that NH₄⁺-N and NO₃⁻-N were key properties affecting soil bacterial and fungal communities. Random forest analysis identified Actinobacteriota, NH₄⁺-N, NO₃⁻-N, Proteobacteria, and S_UR as important factors for plant growth, with Proteobacteria and Actinobacteriota as key microorganisms under WW and DS, respectively.</p> Conclusions <p>This study demonstrated organic fertilizers can effectively improve soil nutrient and enzyme activity, enrich beneficial microbial abundance, and enhance drought resistance of apple seedlings, which can provide basis for understanding the underlying mechanism of the growth-promoting effects of organic fertilizers on apple under normal and drought conditions.</p>