This study assessed the feasibility and benefits of high intensity interval training (HIIT) plus lifestyle education among inactive adults with celiac disease. 41 participants were randomized to receive the intervention (HIIT+) for 12-weeks or waitlist control (WLC). Testing was completed at baseline, immediately post- and 3-months post-intervention. Generalized estimating equations were used to assess changes in the outcome variables over time between the groups. Mean percent of age-predicted maximum heart rate was 97.9% and average rating of perceived exertion (RPE) was 6.33 (out of 10) during HIIT intervals. Following the intervention, the HIIT+ group showed enrichment in relative abundance of Parabacteroides and Defluviitaleaceae_UCG¬_011 while WLC showed enrichment in relative abundance of Roseburia intestinalis, Klebsiella and Adlercreutzia. A unique set of taxa were differentially abundant between the groups at 3-months post-intervention. HIIT+ participants experienced a reduction in resting heart rate (-6.6 bpm) immediately post-intervention compared to WLC. Further research is needed to establish an optimal HIIT protocol that may improve VO2max and metabolic syndrome biomarkers. Findings from this pilot study provide preliminary evidence that a HIIT+ intervention is feasible for inactive adults with celiac disease and leads to favourable changes in resting HR alongside potentially beneficial shifts in gut microbiota. Trial registration number: ClinicalTrials.gov number NCT03520244 Novelty • High intensity interval training leads to potentially beneficial changes in the gut microbiota of adults with celiac disease. • A high intensity interval training exercise intervention is feasible and well tolerated for patients with celiac disease.