There are many factors that contribute to the onset of osteoporosis, and diet is considered to be one of the most important. The fundamentals of preventing osteoporosis include exercise and adequate nutrient intake. However, nonnutritive functional factors found in fruits and vegetables are also gaining attention. These factors are associated with not only the prevention of osteoporosis and other locomotive syndromes but also the prevention of lifestyle-related diseases rooted in chronic inflammation, which is a key factor in metabolic syndrome. This article provides an overview of phytochemicals that regulate bone metabolism and are considered effective for preventing locomotive syndrome. These phytochemicals are categorized by their mechanisms of action. Isoflavones (ISOs), components of soybeans that have been consumed in Japan for a long time, primarily inhibit bone destruction through estrogen-like effects. However, since ISO metabolism is influenced by the intestinal environment, prebiotics that modify intestinal microbiota and ISO metabolism have been identified when taken simultaneously. Their effective regulatory effects on bone metabolism have been demonstrated using osteoporosis model animals. Approximately half of Asians can metabolize isoflavones into equol (Eq), and Eq producers reportedly have a greater protective effect against lifestyle-related diseases. Human intervention studies have confirmed that combining ISO and prebiotic intake improves the ability of non-Eq producers to produce Eq. Additionally, equol has been found to have enantiomers, with the S-form exhibiting a stronger effect on bone metabolism. Furthermore, the preventive effects of phytoestrogens other than isoflavonoids on osteoporosis have been reported. Conversely, citrus flavonoids regulate bone and lipid metabolism through statin-like effects by inhibiting cholesterol synthesis. They have been shown to improve bone, lipid, and glucose metabolism in postmenopausal women, men, and diabetic osteoporosis models. Analyzing the bone metabolism regulation mechanisms of phytochemicals with anti-inflammatory effects and their potential to prevent locomotive and metabolic syndromes based on chronic inflammation has also been suggested.