This meta-analysis aimed to assess the effect of Roux-en-Y gastric bypass (RYGB) on three-dimensionally assessed volumetric bone mineral density (vBMD) with the effect of time on these changes, on bone quality, and the agreement of dual-energy X-ray absorptiometry (DXA) with quantitative computed tomography (QCT) or high-resolution peripheral QCT (HR-pQCT) estimates of bone loss. We searched PubMed, Web of Science, Cochrane, Scopus, and EBSCO. Longitudinal studies on adults undergoing RYGB in which vBMD was assessed by QCT or HR-pQCT with ≥6 months follow-up were included. Total hip (TH) changes were reported in four studies, lumbar spine (LS) in eight, radius in eight, and tibia in seven. Significant post-RYGB vBMD reductions occurred at all skeletal sites analyzed. Meta-regression revealed that time post-RYGB was significantly associated with vBMD deterioration in all skeletal sites except at the TH. RYGB also led to significant deterioration on bone quality. DXA underestimated LS and overestimated TH bone losses post-RYGB. In conclusion, RYGB was associated with significant vBMD loss, which makes screening of bone mass progression by three-dimensional technology a crucial clinical issue to prevent fracture risk and osteoporosis.