We investigated extreme changes in diet patterns on the gut microbiota of elite race walkers undertaking intensified training and its possible links with athlete performance. Numerous studies with sedentary subjects have shown that diet and/or exercise can exert strong selective pressures on the gut microbiota. Similar studies with elite athletes are relatively scant, despite the recognition that diet is an important contributor to sports performance. In this study, stool samples were collected from the cohort at the beginning (baseline; BL) and end (post-treatment; PT) of a three-week intensified training program during which athletes were assigned to a High Carbohydrate (HCHO), Periodised Carbohydrate (PCHO) or ketogenic Low Carbohydrate High Fat (LCHF) diet (post treatment). Microbial community profiles were determined by 16S rRNA gene amplicon sequencing. The microbiota profiles at BL could be separated into distinct “enterotypes,” with either a Prevotella or Bacteroides dominated enterotype. While enterotypes were relatively stable and remained evident post treatment, the LCHF diet resulted in a greater relative abundance of Bacteroides and Dorea and a reduction of Faecalibacterium. Significant negative correlations were observed between Bacteroides and fat oxidation and between Dorea and economy test following LCHF intervention.