Bariatric surgery can lead to short-mid-term vitamin deficiencies, but the long-term vitamin deficiencies is unclear. This study aimed to conduct a meta-analysis regarding the long-term prevalence (≥ 5years) of vitamin deficiencies after bariatric surgery. We searched the EMBASE, PubMed, and CENTRAL databases for clinical studies until June 2023. Meta-analysis, sensitivity, subgroup, and meta-regression analyses were performed. This meta-analysis included 54 articles with follow-up duration ranging from 5 to 17years. The most prevalent vitamin deficiencies after surgery were vitamin D (35.8%), followed by vitamin E (16.5%), vitamin A (13.4%), vitamin K (9.6%), and vitamin B12 (8.5%). Subgroup analyses showed that the prevalence of vitamin A and folate deficiencies increased with the follow-up time. Roux-en-Y gastric bypass had a higher rate of vitamin B12 deficiency than sleeve gastrectomy and biliopancreatic diversion with duodenal switch (BPD-DS). Studies conducted in Europe had higher vitamin A deficiency (25.8%) than in America (0.8%); Asian studies had more vitamin B12 but less vitamin D deficiency than European and American studies. Meta-regression analysis displayed that publication year, study design, preoperative age, BMI, and quality assessment score were not associated with vitamin A, B12, D, and folate deficiencies rate. A high prevalence of vitamin deficiencies was found after bariatric surgery in the long-term follow-up, especially vitamin D, E, A, K, and B12. The variation in study regions, surgical procedures, and follow-up time are associated with different postoperative vitamin deficiencies; it is necessary to develop more targeted vitamin supplement programs.