Abstract Background Addressing cognitive behavioral factors is associated with a favorable development of eating styles (i.e., increased levels of restrained eating, decreased levels of external and emotional eating) in individuals with overweight and obesity. Research suggests that the use of digital interventions that consider gender aspects regarding prevalence, comorbidities, and weight-related behaviors could enhance existing treatment options. This randomized controlled trial aimed to evaluate the effectiveness of the self-guided gender-sensitive mobile health intervention I-GENDO on restrained, emotional and external eating, body mass index, and physical activity at the end of the intervention, and at a 9- and 15-month follow-up. Methods Two hundred thirteen individuals (67% female, body mass index: 33.35 ± 3.79 kg/m²) were randomly assigned to the intervention or control group. Multilevel models were calculated to investigate differences between groups. I-GENDO offered interactive modules addressing psychological content associated with obesity. Users were able to self-tailor intervention content based on their individual needs and life realities. Results Restrained eating was higher in the intervention group after the intervention (95% CI: 0.20, 0.36) and at 9-months (95% CI: 0.07, 0.24). At 9-months, emotional eating among women was lower in the intervention group compared to the control group (95% CI: -0.44, -0,19). In the intervention group, external eating was lower after the intervention, which remained significant for women at 9 (95% CI: -0.40, -0.19) and 15-months (95% CI: -0.34, -0.13). Body mass index of men in the intervention group was 1.44 lower at 15-months than in the control group. No significant effects on physical activity were found. Conclusions The I-GENDO intervention was effective in changing restrained eating of both women and men in the long-term, suggesting that a self-guided, gender-sensitive approach is promising. However, the differential effects on the outcome measures indicate that more research is warranted to examine distinct gender-sensitive mechanisms of digital psychological interventions (i.e., dose–response relationship, blended counselling). Trial registration ClinicalTrials.gov identifier: NCT04080193, 06–09-2019.