Estrogen deficiency can contribute to osteoporosis in postmenopausal women. Phytoestrogens are becoming more widely recognized as potential estrogen replacement therapy. The administration of phytoestrogens can cause bone formation, which is marked by an increase in Runx2 expression in osteoblast cells and can be seen using western blot and immunohistochemistry approaches. This review aimed to compare the detection methods of Runx2 in phytoestrogen-induced bone tissue using western blots and immunohistochemistry. Selectivity, sensitivity, processing time, and cost-effectiveness were the parameters that were compared. This review was done by identifying articles in several databases (Google Scholar, PubMed, and Science Direct). The process of selecting the articles used the PRISMA guidelines to create a flowchart with inclusion and exclusion study criteria. Meta-synthesis was done to analyze, identify, and interpret all of the data in the articles systematically. 70 articles in total were obtained from the selection process, with 21 articles being relevant to the topic. The result shows that the selectivity and sensitivity of western blot for detecting Runx2 on tissue were 93.5–100%, respectively, whereas immunohistochemistry selectivity and sensitivity were 45–99.5%, respectively. Compared to immunohistochemistry, western blot can save up to 57.26%. Immunohistochemistry takes 46 hours to process, while Western blot takes 25 hours and 20 minutes. In comparison to immunohistochemistry, the western blot is more selective, sensitive, rapid and affordable for detecting Runx2 in bone tissue.