Organic substitution improves yield and quality of Zanthoxylum bungeanum by enhancing soil quality index and nutrient accumulation

• M40 % treatment increased the yield of Z. bungeanum by 26.14 %. • M40 % treatment increased the Z. bungeanum quality index by 164.56 %. • M40 % treatment improves SQI by 205.45 %, driving better nutrient uptake (N, K, Ca). • Higher uptake of N, K, and Ca increased yield and improved fruit quality. Excessive chemical fertilization leads to unsustainable Zanthoxylum bungeanum cultivation, which results in yield, quality, and soil quality decrement. Knowledge gaps regarding the effects of organic substitution on the yield and quality of Zanthoxylum bungeanum require further investigation. The two-year field experiment evaluated the effects of different organic substitution ratios on Zanthoxylum bungeanum yield, quality index (ZQI), and soil quality index (SQI). Five fertilization treatments were designed, including control, farmer’s practice, optimized fertilization, and two substitution ratios replacing 20% and 40% of chemical nitrogen with organic fertilizer. The results showed that the 40% organic substitution significantly enhanced the yield and quality of Zanthoxylum bungeanum by 26.14% and 124.56% respectively, compared with farmer’s practice. The M40% treatment resulted in the highest SQI, which was significantly elevated by 127.02%, compared with farmer’s practice. Analysis result of redundancy and partial least squares path showed that organic substitution positively influenced the yield and quality of Zanthoxylum bungeanum through direct improvement in soil quality (path coefficient = 0.63) and indirect increments of leaf calcium concentration (0.95), fruit potassium (0.95) and nitrogen absorption (0.93). Our study revealed the corresponding mechanisms of partial organic substitution affecting SQI changes and improving Zanthoxylum bungeanum yield and quality. In conclusion, partial organic substitution presents a practical approach to Zanthoxylum bungeanum sustainable production in Southwest China.