Apple production is a globally significant agricultural activity, and optimizing yield and quality is essential for sustainability. However, yield limitations in many regions often stem from inadequate soil property assessments and overreliance on chemical fertilization. This study evaluated the physical, chemical, and biological components of soil quality in 20 semi-dwarf apple orchards in Karaman, Turkey. Soil samples were collected at depths of 0–30 cm and 30–60 cm, and 36 analyses were conducted. The minimum data set included microporosity, total porosity, and least limiting water range for physical quality; electrical conductivity, iron, copper, and calcium for chemical quality; and nitrate, potentially mineralizable nitrogen, and activated carbon for biological quality. Nonlinear scoring functions were applied, yielding mean physical, chemical, and biological quality scores of 0.46, 0.88, and 0.67, respectively. While chemical quality was high, physical and biological quality remained low to moderate, contributing to yield decline. Correlation analysis (R² = 0.8076) revealed that orchards with high chemical scores experienced yield losses due to poor physical quality. These findings highlight the necessity of improving soil quality, particularly physical and biological aspects, to ensure sustainable apple production.