Limonin has been shown to exert anti-inflammatory effects, however, its roles in tumor progression remain unclear. This work aims to investigate the roles and related mechanism of limonin in the stemness of breast cancer cells. Here, we found that limonin attenuated the stemness of breast cancer cells in a concentration-dependent manner, evident by the decreasing the capacity of cell spheroid formation, expression of stemness markers and ALDH1 activity, whereas had no toxicity on non-tumorigenic cells. Additionally, limonin enhanced adriamycin sensitivity of breast cancer cells and attenuated adriamycin resistance in adriamycin-resistant breast cancer cells. Mechanistically, limonin decreased MIR216A methylation level and thus increased miR-216a-3p expression. Furthermore, miR-216a-3p could directly bind to WNT3A and thus inactivated Wnt/β-catenin pathway. Therefore, our results indicate that limonin could attenuate the stemness and chemoresistance via inhibiting MIR216A methylation and subsequently suppressing Wnt/β-catenin pathway.