Background: Intellectual disability (ID) is a neurodevelopmental disorder associated with a poorer health profile and higher mortality. Young people with ID have more sedentary lifestyles than their typically developing peers. Consequently, this group is at significant risk of developing lifestyle diseases (ie, noncommunicable diseases) later in life. Increasing physical activity and eating a healthier diet have been argued to be effective ways to improve the health of adolescents and young adults with ID. Digital interventions are a viable option for improving health behaviors. Objective: This research protocol describes a co-design approach using workshops to develop a digital intervention that promotes healthy behaviors, including increasing physical activity and eating a healthier diet, among adolescents and young adults with ID. Methods: A participatory design using a co-design approach will be applied as a strategy to include potential users of the digital intervention and other stakeholders in the research process, comprising research design, data collection, and data analysis. A total of 7 to 10 workshops will be conducted aimed at developing a digital intervention and will include procedures for assessing needs; facilitators and barriers to health promotion; physical, mental, and social well-being; participation; and relationships. The workshops will include 12 to 18 stakeholders with experience of clinical practice and research related to young people with ID, including relatives, as well as adolescents and young adults (aged 16-25 years) with mild to moderate ID. Participants will perform a mixture of individual and group work using whiteboards, sticky notes, felt-tip pens, cards, balls, stickers, and wireframe templates. Data analysis will take place concurrently with data collection as an iterative process. Transcribed data from the audio and video recordings of the groups’ discussions will be analyzed following a qualitative methodological procedure. Results: This study protocol provides a systematic record of the scientific methodologies used when developing the digital intervention and provides insights into the potential practical solutions and challenges when following a co-design approach in which relatives and professionals, as well as adolescents and young adults with ID, are included as research partners. Recruitment of participants started in April 2023. Data collection, analysis, and reporting will be completed in December 2023. Conclusions: This study will explore the effectiveness of workshops at gathering rich, reliable, and valid data in a co-design approach with participants. The results will provide increased knowledge in how to use technology to develop novel, evidence-based, and scalable interventions that adolescents and young adults with ID can and want to use to motivate physical activity and a healthier diet. The project will provide a simple and cognitively accessible digital solution for promoting lifestyle behaviors tailored to the needs of adolescents and young adults with ID.