Research on gut-microbiota (GM) changes in infants and children with intestinal surgical conditions, and how these changes might leverage to improve outcomes, is progressing rapidly. Nonetheless, there is a lack of information regarding the role of GM following surgery for the most prevalent intestinal pediatric disorders that necessitate surgical intervention, despite it receiving considerable interest. Pre-surgical dysbiosis and post-surgical GM assessment of these disorders are still poorly understood. This detailed review has gathered insights into the current understanding of unique alterations in GM colonization following surgery for significant childhood conditions, such as necrotizing enterocolitis (NEC), Hirschsprung’s disease (HD), inflammatory bowel disease (IBD), and short bowel syndrome (SBS).In particular, surgery for NEC may result in a reduction in GM diversity. Surgical procedures for HD can alter the GM, potentially causing shifts in GM compositions and increasing the likelihood of complications such as Hirschsprung’s associated enterocolitis (HAEC). For children diagnosed with IBD, surgical interventions can bring about changes in the diversity and structure of GM, which may lead to disease recurrence or affect the success of treatment. Children with SBS, following extensive bowel resections, display abnormal GM profiles when compared to healthy children. These GM patterns may include diminished. GM diversity, an increase in inflammation-related bacteria, and a decrease in beneficial bacteria. Moreover, the most common complications that occur after surgical procedures for the above-mentioned intestinal disorders are greatly affected by the GM. Current research provides an initial understanding of the possible post-surgical implications for outcomes of these intestinal disorders. Future studies could clarify GM alterations associated with various intestinal paediatric surgical procedures and their complications, which may influence the evaluation of GM-targeted treatments.