Background People with intellectual disabilities (ID) have low levels of physical activity (PA) together with accelerated aging profiles. Adherence to PA interventions for persons with ID is low based on barriers such as motivation. The IDEA study aims to determine the effect of two types of exercise programs, continuous aerobic (CAEP) vs sprint interval training (SIT), designed for seniors with ID on health-related physical fitness, cardiovascular parameters, quality of life (QoL), and emotional and cognitive function. Methods In this trial, ninety seniors with ID between the ages of 40 and 75 yrs. from occupational health centers from the Autonomous Region of Catalonia (Spain) will be recruited. Participants will be randomly allocated to the CAEP, SIT, and control group. Both intervention groups will train 3 days/week, 1.5 h/day over 6 months. Outcome variables will be assessed at baseline, 6 months and 12 months. The outcome variables include weight, height, body composition, cardiorespiratory fitness, muscle strength, balance, flexibility, cardiovascular parameters (blood pressure, pulse-wave velocity, pulse-wave analysis), QoL and cognitive function. The intervention effect will be determined with mixed models with repeated measures to assess changes in the outcome variables over time (baseline to month 12) and between study arms. Relationship between variables will be analyzed with appropriate regression analyses. Discussion Various studies reported on CAEP and SIT as exercise interventions for persons with ID with beneficial outcomes on body composition, fitness and blood pressure. To our knowledge, this is the first trial designed to analyse the positive changes on fitness, PA levels, cardiovascular, QoL and cognitive function promoted by CAEP training and SIT in seniors with ID. The findings of this study will assist in the development of more effective exercise interventions to ensure better compliance and adherence to exercise in seniors with ID.