Introduction Total mesorectal excision is the standard of care for rectal cancer, which can be performed using open, laparoscopic, robot-assisted and transanal technique. Large prospective (randomised controlled) trials comparing these techniques are lacking, do not take into account the learning curve and have short-term or long-term oncological results as their primary endpoint, without addressing quality of life, functional outcomes and cost-effectiveness. Comparative data with regard to these outcomes are necessary to identify the optimal minimally invasive technique and provide guidelines for clinical application.Methods and analysis This trial will be a prospective observational multicentre cohort trial, aiming to compare laparoscopic, robot-assisted and transanal total mesorectal excision in adult patients with rectal cancer performed by experienced surgeons in dedicated centres. Data collection will be performed in collaboration with the prospective Dutch ColoRectal Audit and the Prospective Dutch ColoRectal Cancer Cohort. Quality of life at 1 year postoperatively will be the primary outcome. Functional outcomes, cost-effectiveness, short-term outcomes and long-term oncological outcomes will be the secondary outcomes. In total, 1200 patients will be enrolled over a period of 2 years in 26 dedicated centres in the Netherlands. The study is registered at https://www.trialregister.nl/9734 (NL9734).Ethics and dissemination Data will be collected through collaborating parties, who already obtained approval by their medical ethical committee. Participants will be included in the trial after having signed informed consent. Results of this study will be disseminated to participating centres, patient organisations, (inter)national society meetings and peer-reviewed journals.