Background: It is expected that in 2020 more than 17,000 cases of colorectal cancer will be diagnosed in The Netherlands. To date, patients are included in a surgeon-led follow-up programme whose main focus is recurrence detection. However, patients often experience multiple physical and psychosocial problems. Currently, these problems are not always encountered. More care by a generalist is suggested as a solution. Furthermore, patients prefer to undergo rehabilitation in their own environment and to be more involved in their own health care. eHealth applications might enhance this. Oncokompas2.0 is an online self-management application which facilitates access to supportive care. This study aims to evaluate primary care follow-up and aftercare in comparison with secondary care follow-up and aftercare for patients with colon cancer. Second, the added value of Oncokompas2.0 to care will be assessed. Methods/Design: This is a multi-centre 2 × 2 factorial randomised controlled trial with a calculated sample size of 300 patients. Patients with stage I, II, or III colon carcinoma are eligible. Patients will be randomly assigned in four groups: (1) usual follow-up visits and aftercare provided in secondary care, (2) usual follow-up visits and aftercare provided in secondary care with additional use of Oncokompas2.0, (3) follow-up and aftercare in primary care, and (4) follow-up and aftercare in primary care with additional use of Oncokompas2.0. The primary outcome is quality of life. Secondary outcomes include physical outcomes, psychosocial outcomes, number of investigations, referrals and related communication between secondary and primary care, (time of) recurrence detection and protocol adherence, attention to preventive care, self-management of patients, patient satisfaction, and preference of care at the end of the trial. Data collection will be done by questionnaires and extractions from electronic medical records. Discussion: The results of this study will provide evidence, which has been scarce to date, on prominent general practitioner involvement in care for colon cancer patients after initial treatment. Also, it evaluates the efficacy of an eHealth application to enhance patient empowerment.