Background: Food allergies (FAs) are an increasing public health concern, particularly in children. Oral immunotherapy (OIT) is an emerging treatment strategy under clinical investigation for desensitization of children with FA to food allergens. Dysbiosis of the gut microbiota has been implicated in FAs, and various factors influence its composition; however, the impact of OIT on the gut microbiota remains largely unexplored. Objective: This study aimed to identify the changes in diversity of the gut microbiota following OIT in children with FA. Methods: Thirty children with FA undergoing oral immunotherapy and seven non-allergic controls participated in this study. Fecal samples were collected before and after OIT from children with FA, and once from controls. The gut microbiota was profiled using 16S rRNA sequencing, followed by diversity and differential abundance analyses. Alpha and beta diversities were compared, and differential abundance was assessed. Results: Beta diversity analysis revealed small but significant differences in microbial composition between children with FA before and after OIT, and between controls and children with FA before OIT. Differential abundance analysis showed that OIT induced a reversion of the abundance levels of Bacteroidota and Verrucomicrobiota towards those observed in controls. Conclusion: To our knowledge, this is the first study to investigate the impact of OIT on the gut microbiota in children with different FAs for identifying potential microbial biomarkers, and convincingly demonstrated their interrelation. These findings may help improve and personalize FA treatment.