Background: Gastrointestinal symptoms (GISs) can affect the performance of endurance athletes (EAs). This study aims to analyze the efficacy of carbohydrate (CHO), gluten-free, and low-mono-saccharide and polyol (FODMAP) diets in preventing GISs in adult EAs of both sexes. Methods: A systematic search was conducted prior to 30 June 2024 in accordance with the PRISMA statement. We searched for original studies from the last eight years, in English or Spanish, that looked at the effect of CHO, gluten-free, or FODMAP diets on the GISs of EAs. In PubMed, the MeSH (medical subject heading) categories were used. The search was repeated in EBSCO, Google Scholar, and Web of Science. The inclusion criteria were determined using the PICOS framework and the risk of bias in each paper was assessed using the PEDro scale quality criteria checklist (systematic review registration: INPLASY202490080). Results: Of 289 articles identified, only 3.5% met the eligibility criteria. All studies found that GISs are common in EAs. We found that 60% of the articles used an experimental method; moreover, based on 80% of the articles, following a bowel training diet, like CHO, reduced fiber and dairy products, or a low-FODMAP diet, has the potential to reduce gastrointestinal symptoms and improve the athletic performance of EA. Conclusions: We found that low-FODMAP diets, gut training with CHO intake, and decreased fiber and dairy intake may have favorable effects in preventing GISs. No studies support a gluten-free diet in reducing GISs in EAs.