Aims/hypothesis <p>Homozygous carriers of a loss-of-function variant in the sucrase-isomaltase (SI) gene (c.273_274delAG) are unable to digest sucrose and parts of starch. The variant is common only in Indigenous Arctic populations such as the Greenlandic Inuit and has been associated with a healthier metabolic profile. In a unique gene–diet intervention, we aimed to study whether the <i>SI</i> genotype modulates the effect of two different diets on glucose homeostasis and lipids.</p> Methods <p>A genotype-based randomised crossover trial was conducted in homozygous <i>SI</i> carriers and non-carriers in Nuuk and Maniitsoq (Greenland), with two 3 day interventions and a 7 day wash-out period. Participants were ≥18 years, had no gastrointestinal disorders, diabetes nor carried an Inuit-specific high-risk type 2 diabetes variant in <i>TBC1D4</i>. The interventions were as follows: a Greenlandic fish- and meat-rich diet; and an isoenergetic Western diet with 11% energy from sucrose. The order of the diets was randomised by the participants using a dice and participants and personnel were not blinded. The primary outcome was glucose variability measured as CV. Fasting blood samples were drawn before and after each intervention for measurement of lipids, insulin and C-reactive protein. We assessed genotype × diet interaction effects using linear mixed models. The study was reported in accordance with the CONSORT 2010 statement: extension to randomised crossover trials and the consolidated criteria for strengthening reporting of health research involving Indigenous peoples (the CONSIDER statement).</p> Results <p>Seventeen carriers and 16 non-carriers completed the intervention. CV was higher on the Western diet than on the Greenlandic diet for non-carriers (β=5.23% [95% CI 3.02, 7.45]) but not for the carriers (β 1.27% [−0.86, 3.4]). Carriers had a 20% lower CV on the Western diet compared with non-carriers (<i>p</i>_{genotype×diet}=0.015). Carriers had lower fasting insulin levels than non-carriers at baseline, and the Greenlandic diet decreased the levels in non-carriers by 22.7 pmol/l (95% CI 5.1, 40.3) but not in carriers (<i>p</i>_{genotype×diet}=0.009). We observed no <i>SI ×</i> diet interaction effects on lipids levels.</p> Conclusions/interpretation <p>Homozygous loss-of-function <i>SI</i> carriers show better glycaemic management than non-carriers on a Western diet, suggesting SI inhibition as a potential treatment target.</p> Trial registration <p>ClinicalTrials.gov NCT05375656</p> Funding <p>Independent Research Fund Denmark, Greenland Research Council and Brugseni.</p> Graphical Abstract <p></p>