In rainfed apple orchards on China's Loess Plateau, water limitation and soil fertility decline jointly constrain productivity, while conventional surface fertilization often fails to effectively improve deeper soil conditions and achieve efficient nutrient supply. Deep trench application of organic fertilizer combined with microbial inoculants offers a new management option; however, its integrated effects on soil structure and water retention, nutrient supply, apple yield, and soil quality remain insufficiently evaluated. We conducted a two-year rainfed field trial in an apple orchard on a loess-derived Calcaric Cambisol to test whether deep trench application of organic fertilizer combined with microbial inoculants improves soil quality and apple (Malus domestica) productivity, using five treatments: no organic fertilizer or inoculant (CK), deep trench application of organic fertilizer alone (OD), and OD supplemented with heterotrophic bacteria (ODH), photosynthetic bacteria (ODP), or a compound microbial inoculant (ODHP). The ODHP significantly increased organic carbon content by 18.68% and total nitrogen content by 16.94% in the 0-40 cm soil layer, while decreasing the proportion of silt-sized particles by 6.03% in the 20-40 cm layer compared to the OD treatment. ODH increased NO3--N content by 27.14% and carbonate content by 23.15% in the 20-40 cm soil layer compared to OD. ODHP treatment boosted apple yield by 32.59% relative to OD. Soil quality index (SQI) values under organic fertilization increased by 34.00%-93.00% compared to the CK, with ODHP exhibiting the highest improvement, followed by ODH. Partial least squares path modeling revealed that the improvement in soil physicochemical properties majorly influenced yield increase by positively regulating soil biological activity, with urease and alkaline phosphatase activities being the key driving factors affecting yield. Overall, trench application of organic fertilizer with compound microbial inoculants can improve soil quality and apple productivity in rainfed loess orchards, but its long-term and broader applicability requires multi-year, multi-site validation.