Bariatric surgery (BS) is an effective intervention for obesity and related metabolic disorders, significantly improving metabolic health and alleviating hormonal imbalances. However, it induces complex endocrine changes that can lead to dysfunctions, impacting the somatotropic, gonadal, thyroid, pancreatic, and adrenal axes. This review highlights the dual effects of BS on the endocrine system. A comprehensive review of peer-reviewed studies using PRISMA guidelines was conducted, focusing on human research evaluating pre and postoperative endocrine parameters. Studies were selected for their relevance and quality in elucidating the endocrine consequences of BS. BS restores growth hormone secretion and improves fertility but may disrupt insulin-like growth factor-1 recovery and sex hormone balance, leading to bone loss and catabolic states. Postprandial insulin hypersecretion can result in hyperinsulinemic hypoglycemia, with impaired counter-regulatory hormone responses. Secondary hyperparathyroidism and reduced bone density highlight additional risks. Changes in thyroid hormone levels have implications for both hypothyroid and euthyroid patients. These findings underscore the interplay between improved metabolic control and potential endocrine dysfunctions. The current evidence predominantly comprises association studies that may not be of quality for safe clinical decision-making, highlighting the need for high-quality research to establish causality and refine therapeutic strategies. Bridging knowledge gaps in the mechanisms underlying these changes is crucial to optimizing BS outcomes. A holistic approach integrating preoperative screening, individualized postoperative care, and targeted therapies is essential to mitigate complications while maximizing benefits.