Dietary restriction of certain fermentable carbohydrates (low fermentable oligosaccharides, disaccharides, monosaccharides and polyols (FODMAP) diet) is effective for managing symptoms of irritable bowel syndrome (IBS). However, there are potential consequences of this diet that relate to its impact on nutritional, microbiological, and health-related quality of life outcomes. Evidence suggests that the low FODMAP diet leads to some alterations in nutrient intake. For example, carbohydrate intake is reduced, and there is a decrease in the proportion of patients meeting the recommended intake for calcium. Intake of other macro and micro-nutrients appears to be adequate in the short term. As well as the impact on nutrient intake, extensive dietary modification can have a pronounced impact on the gastrointestinal microbiota. Indeed, recent data suggests the diet markedly reduces luminal Bifidobacteria concentration, and there is limited evidence that it reduces total bacteria abundance and concentration of other bacterial groups, for example, Faecalibacterium prausnitzii. Finally, despite the evidence for its clinical effectiveness in patients with IBS, the restrictive nature of the diet could pose a significant burden on patients, thereby limiting improvements, or indeed worsening health-related quality of life. In conclusion, while robust evidence supports the clinical effectiveness of the low FODMAP diet, it is important, considering the likelihood of its continued widespread use in IBS and other functional bowel disorders, that we extend our understanding of the impact of the diet on endpoints that may have potential consequences for long term health.