Proton pump inhibitors (PPIs) are one of the most commonly prescribed drug groups in developed countries. Their approved indications include gastroesophageal reflux disease, peptic ulcer disease, and prophylaxis against NSAID-induced gastroenteropathy in specific scenarios. Since their introduction into clinical practice, their usage has significantly increased, leading to concerns about possible inappropriate prescribing, which can result in a higher risk of side effects and increased economic costs. Consequently, in recent years, literature linking PPIs to various adverse effects has emerged, with some supported by robust evidence, while others are based on lower-quality evidence, requiring cautious interpretation. Among the adverse effects of PPIs, significant ones include an increased risk of fragility fractures, deficiencies in certain micronutrients such as vitamin B12 and magnesium, a higher incidence of enteric infections, especially Clostridioides difficile, complications in cirrhotic patients, and pharmacological interactions with other medications. In clinical practice, it is essential to periodically evaluate the rationale for prescribing these drugs and consider discontinuing them if there is no appropriate indication. Despite PPIs being generally safe medications, it is crucial to be aware of their potential adverse effects and appropriate indications to ensure their proper use.