<p>Applications of biochar and organic fertilizer have been reported as a beneficial practice for improving soil quality and crop productivity. However, whether such synergy can improve soil quality and leaf yield in a wheel wingnut and tea composite system at acid soil site remains unknown. Therefore, a field experiment was conducted to explore the effects of CK (no addition), sole organic fertilizer (100% organic fertilizer, T1), and three kinds of ratio of biochar and organic fertilizer (15% biochar + 85% organic fertilizer, T2; 30% biochar + 70% organic fertilizer, T3; 50% biochar + 50% organic fertilizer, T4, w/w) on soil physicochemical properties, enzyme activities and leaf yield in the composite system. Results indicated that in the 0–10&#xa0;cm layer co-applications of biochar and organic fertilizer improved soil pH by 2.3–14.2%, whereas soil available nitrogen and phosphorus increased by 21.7–165.6% and 9.5–24.1% in both sole organic fertilizer and the co-application treatments respectively, when compared with CK. However, only T4 significantly increased soil available potassium by 41.8%, and T2 significantly decreased soil bulk density and increased total porosity. Generally, the treatments of T1, T2, and T3 enhanced the activities of C–, N–, and P-acquiring enzymes, thus decreasing soil N:P_EEA and increasing soil enzyme vector angle, and alleviating soil microbial N limitation. Compared with CK, the treatments of T1, T2, and T3 increased leaf yield of the composite system by 4.1–20.7% but decreased by 6.1% in T4. Random forest model identified soil β-glucosidase (<i>P</i> &lt; 0.05), acid phosphatase (<i>P</i> &lt; 0.01), and soil available potassium (<i>P</i> &lt; 0.05) as the primary factors governing leaf yield in the composite system. PLS-PM model (GOF = 0.527) indicated that co-application of biochar and organic fertilizer increased the leaf yield in the composite system, mainly by alleviating soil microbial N limitation and further improving the soil quality index.</p>