Background: This study aimed to investigate the impact of prolonged exposure to PPIs on the gastrointestinal microbiota, as well as to assess its potential implication on the development of gastrointestinal diseases. Methods: This literature review was based on the "National Library of Medicine” (PubMed) research platform, using the descriptors (intestinal microbiota OR gastrointestinal microbiomes OR gut microbiota OR gastrointestinal flora) AND (Proton pump inhibitors OR PPIs). The applied filters for work selection were: published within the last 5 years; written in Portuguese, English, or Spanish; excluding systematic reviews and meta-analyses. Results: Recent studies have revealed a series of alterations in the gastrointestinal microbiota, which have been associated with the exacerbation of pre-existing pathologies or the onset of new conditions. Prolonged use of PPIs has shown considerable impacts on the quantity of gastrointestinal microorganisms such as Streptococcus, Lactobacillus, Bacteroidetes, Veillonellaceae, among others. In addition, an increased incidence of diseases such as hepatic encephalopathy, gastroesophageal reflux disease (GERD), cirrhosis, spontaneous bacterial peritonitis, and intestinal infections have been found. Conclusion: The results showed that the dysbiosis triggered by chronic use of PPIs leads to an increased risk of gastrointestinal diseases. Therefore, it is crucial to adopt a rational prescription of these drugs, carefully considering the risks and benefits to ensure safe and effective use in clinical practice. Furthermore, there is a need for further research to define possible risk groups related to chronic use of PPIs, such as patients with hepatic cirrhosis or hepatitis B