Background: Soybean cultivars grown on various crop rotation models in the agroforestry system with kayu putih (Melaleuca cajuputi) have shown different yields per hectare. However, no information related to morpho-physiological and biochemical fingerprints affecting soybean yield has been found. Thus, this study aimed to determine the morpho-physiological and biochemical fingerprints and their effect on the soybean agroforestry system in different crop rotation models through multivariate analysis. Methods: The study was conducted during the dry season (March-June 2021) and the wet season (November 2021-February 2022) in Menggoran Forest Resort, Playen Forest Section, Yogyakarta Forest Management District, Indonesia. The morpho-physiological and biochemical variables of 15 soybean cultivars were evaluated using four crop rotation models. Observations included 22 morphological, physiological and biochemical variables of soybean. Data were analyzed using ANOVA, PCA-biplot, heatmap cluster, factor analysis, SEM-PLS and standardized stepwise regression. Result: Results showed four groups of soybean cultivars and three groups of crop rotation models based on morpho-physiological and biochemical fingerprints. Morpho-physiological and biochemical fingerprints of soybean can be differentiated based on root surface area, nitrogen content and superoxide dismutase.