Abstract: Background and Objective: Soil quality assessment is one way to formulate strategies to improve the quality and sustainability of land and productivity of the crop. This study aimed to determine parameters of soil quality that affect the yield of cloves, cocoa and cardamom in the agro-forestry system in Menoreh mountains area. Methodology: The stratified random sampling method was used during the research by stratifying the types of soil stratification in Menoreh mountains area, Samigaluh district, Kulonprogo regency, i.e. Yogyakarta, Indonesia that were Lithic Eutrudept, Vertic Haplustalf and Typic Hapludult. The observations were made on 24 physical, chemical and biological properties of soil and the yield of clove, cacao and cardamom. The determination of soil quality indicator was done by using one-way ANOVA at α 5%, factor analysis and standardized stepwise regression. Results: The result shows that the highest dry weight of clove flowers is produced in the soil type of Vertic Haplustalf, sequentially followed by soil types of Typic Hapludult and Lithic Eutrudept. The highest dry weight of cocoa beans and cardamom bulb is produced in the soil type of Vertic Haplustalf, sequentially followed by soil types of Lithic Eutrudept and Typic Hapludult. Conclusion: The dry weight of clove flowers is affected by the percentage of silt fraction of the soil. The dry weight of cocoa beans is influenced by the content of CEC, Ex-Ca and Ex-Na, while the dry weight of cardamom bulbs is influenced by the content of Ex-Ca.