Bariatric surgery (BS) is the most effective treatment for severe obesity and it has beneficial effects on glycemic control and metabolism outcomes. However, the effects of BS on nutritional outcomes are controversial. Therefore, we aimed to evaluate the changes in several nutritional outcomes after Roux-en-Y gastric bypass (RYGB). A comprehensive search was performed using the following databases: PubMed, Embase, Web of Science, Cochrane Library, WanFang and Chinese National Knowledge Infrastructure. The following outcomes were evaluated: vitamin A, 25-hydroxyvitamin D [25(OH)D], calcium, phosphorus, parathormone (PTH), iron, ferritin, vitamin B12, folate, and zinc. The pooled outcomes were expressed as standard mean difference (SMD) and 95% confidence interval (CI) using a random effects model. Fifty-six studies including 5645 individuals with obesity met the inclusion criteria. Serum 25(OH)D (SMD = 0.78, 95%CI 0.38 to 1.20, P < 0.001), phosphorus (SMD = 0.48, 95%CI 0.22 to 0.74, P < 0.001), PTH (SMD = 0.35, 95%CI 0.11 to 0.59, P = 0.005), vitamin B12 (SMD = 1.11, 95%CI 0.41 to 1.80, P = 0.002), and folate (SMD = 1.53, 95%CI 0.77 to 2.28, P < 0.001) significantly increased after RYGB compared with the baseline. Serum ferritin (SMD = - 1.67, 95%CI - 2.57 to - 0.77, P < 0.001), vitamin A (SMD = - 0.64, 95%CI - 0.99 to - 0.29, P < 0.001), and plasma zinc (SMD = - 0.58, 95%CI - 1.09 to - 0.06, P = 0.027) significantly decreased after RYGB. No significant changes in serum calcium (SMD = - 0.14, 95%CI - 0.40 to 0.11, P = 0.219) and iron (SMD = 0.26, 95%CI - 0.11 to 0.64, P = 0.165) were observed after RYGB. Despite the increased levels of 25(OH)D, phosphorus, vitamin B12 and folate, this meta-analysis revealed the unfavorable nutritional consequences after RYGB.