Background Gastric bypass (GB) and sleeve gastrectomy (SG) are two common types of bariatric surgery that carry many potential complications. Among these complications, bone metabolism-related diseases have attracted substantial attention; however, no meta-analysis of them has been performed to date. Methods We searched PubMed, Web of Science, The Cochrane Library, and Embase to identify relevant studies published before January 2019. The following indicators were evaluated: serum parathyroid hormone (PTH), calcium, phosphorus and 25hydroxyvitamin D levels, body mass index (BMI), and bone mineral density (BMD). Results Thirteen studies met our inclusion criteria. Overall results showed that patients undergoing GB had lower levels of 25hydroxyvitamin D (MD = − 1.85, 95% CI (− 3.32, − 0.39) P = 0.01) and calcium (MD = − 0.15, 95% CI (− 0.24, − 0.07) P = 0.0006) as well as higher levels of PTH (MD = 3.58, 95% CI (0.61, 7.09) P = 0.02) and phosphorus (MD = 0.22, 95% CI (0.10, 0.35) P = 0.0005). The results of BMI and BMD were comparable in each group. Conclusion Our meta-analysis suggested that obese patients undergoing GB had lower levels of serum calcium and 25hydroxyvitamin D as well as higher levels of serum phosphorus and PTH. To prevent postoperative bone metabolism-related diseases, appropriate postoperative interventions should be undertaken for particular surgical procedures.