Probiotics are known to have favorable effects on human health. Nevertheless, probiotics are not always beneficial and can cause unintended adverse effects such as bacteremia and/or inflammation in immunocompromised patients. In the present study, we investigated the effects of probiotics on the regulation of bone metabolism under different health conditions and delivery routes. Intragastric administration of Lactiplantibacillus plantarum to ovariectomized mouse models for mimicking post-menopausal osteoporosis in humans substantially ameliorated osteoporosis by increasing bone and mineral density. In contrast, such effects did not occur in normal healthy mice under the same condition. Interestingly, however, intraperitoneal administration of L. plantarum induced bone destruction by increasing osteoclast differentiation and decreasing osteoblast differentiation. Furthermore, when L. plantarum was implanted into mouse calvarial bone, it potently augmented bone resorption. Concordantly, L. plantarum upregulated osteoclastogenesis and downregulated osteoblastogenesis in in vitro experiments. These results suggest that L. plantarum can have distinct roles in the regulation of bone metabolism depending on bone health and the delivery route.