Soybean elicited with microorganisms transforms its phytochemical content which is rich in anti-inflammatory action. However, the potential effect of the elicited soybean extract (ESE) on the maintenance of the stromal-derived factor-1 (SDF-1) regulatory system in the spleen, thymus, hepar, and bone marrow in high-fat/fructose diet (HFFD) mice is yet to be investigated. In our study, the spleen, thymus, hepar, and femurs were collected and isolated at the end of the experiment. The expression of SDF-1 in hepar, CD4+, CD8+, T cells, and B220+ cells was measured using flow cytometry analysis. To determine the interaction between the active compound of ESE and CXCR4, docking analysis was conducted using PyRx 0.8. The expression of splenic and thymic CD4+SDF-1+, CD8+SDF-1+, and hepatic SDF-1+ was elevated in HFFD mice but not in normal diet (ND) mice. ESE had significantly declined (P < 0.05) in CD4+SDF-1+ and CD8+SDF-1+ T-cells subsets. ESE treatment improved the development of B cells in HFFD mice. The molecular docking analysis identified glyceollin I with the strongest affinity of −8.4 kcal/mol. The results suggest that glyceollin I has a positive effect as a CXCR4 inhibitor. ESE supplementation was significant in maintaining the regulatory system of SDF-1 expressed by CD4+, CD8+, hepatocyte, and B220+ cells in HFFD associated with obesity Keywords: CXCR4, Glyceollin, High-fat, High-fructose, SDF-1, Soybean