Rapidly accumulating evidence supports the important role of gut microbiome in the regulation of mood, behaviour, appetite, gastrointestinal symptomology, and nutrient metabolism. These are all core features frequently altered in individuals with anorexia nervosa (AN). Current treatment recommendations for AN support the use of high-calorie diets as an essential part of nutritional rehabilitation, commonly achieved by elevating the fat content of the diet. However, in contrast to this approach, there is accumulating evidence suggesting the importance of balanced, high-fibre diets on the gut microbiome. Studies have demonstrated profound differences in the microbial composition of underweight people with AN and those of normal- or overweight individuals. Specific alterations vary widely between studies. It is thus far unclear to what extent the observed differences are brought on by iatrogenic effects of nutritional rehabilitation or the disorder itself. To date, only two studies have investigated the changes in the intestinal microbiota during nutritional rehabilitation and corresponding weight restoration. These studies suggest that the gut microbiome of AN patients was different to healthy controls both prior and following nutritional rehabilitation, though it is noted that these states were associated with lower and higher nutritional intakes, respectively. There is a clear need for further investigation regarding the effects of nutritional rehabilitation on the gut microbiome. Such research would provide insights into the potential role of gut microbiome in modulating the pathophysiology of AN and inform future treatment strategies.