Gastrointestinal surgery complications are common. Implementation of an interdisciplinary prehabilitation program could reduce their frequency and shorten hospital stays. Including gut microbiota support supplements in prehabilitation may be a new strategy to reduce treatment-related morbidity in patients undergoing gastrointestinal surgery. The current state of knowledge and previous studies are very heterogeneous in terms of interventions and results obtained. All studies indicate a positive impact of the use of supplements supporting gut microbiota in the perioperative period on the patient’s condition, as well as a reduction in postoperative morbidity, but they do not explain the effect of the microbiota on the entire prehabilitation process. Implementing nutritional interventions together with gut microbiota support supplements from the very beginning of prehabilitation could improve quality of life and reduce complications. The aim of this review is to determine the possibilities of supporting the gut microbiota in the perioperative period for patients requiring gastrointestinal surgery.