Long-term peach cultivation depletes soil nutrients, reduces microbial activity, and decreases organic matter, thereby affecting fruit quality. A field experiment was conducted to explore the effects of soil conditioner application combined with fertilization and water management on soil properties, organic carbon fractions, microbial biomass C/N, water-stable aggregates, and peach quality. Six treatments were designed: no fertilization (CK), farmers’ conventional fertilization with regular water management (NPK+W), farmers’ conventional fertilization combined with optimized water and fertilizer management (NPK+MW), soil conditioner application with regular water management (BGA+W), soil conditioner application combined with optimized water and fertilizer management (BGA+MW), and a combined treatment of 50% soil conditioner + 50% conventional fertilizer with optimized water and fertilizer management (H-BGA+NPK+MW). The results showed that BGA+MW significantly reduced soil pH (6.96%-13.53% during fruit expansion; 7.08%-16.77% at maturity), and increased nitrate-N (15.2%-310.7%) and ammonium-N (236.1%-315.5%). H-BGA+NPK+MW decreased soil bulk density (10.69%-11.36% during expansion; 7.80% at maturity) and improved aggregate stability, with average weight diameter (MWD) and geometric mean diameter (GMD) increased by 32.3% and 100% (expansion) and 3.3% and 9.8% (maturity), respectively. Treatments enhanced organic carbon fractions and soil microbial biomass carbon. NPK+W increased soil organic carbon (SOC) by 31.77% compared with BGA+W during expansion, while H-BGA+NPK+MW showed the highest SOC at maturity. NPK+MW promoted microbial biomass carbon in expansion, and H-BGA+NPK+MW did in maturity. H-BGA+NPK+MW increased soluble solids, and BGA+MW increased soluble sugars. The BGA soil conditioner improves soil microbial activity, organic carbon fractions, and fruit quality in continuous cropping orchards, supporting sustainable production.