BACKGROUND: Epidemiological studies conducted in various parts of the world have clearly demonstrated that metabolic syndrome (MetS) is an increasing global health problem, not only in Western societies but also in Asian populations. Web-based and mobile phone-based self-management applications have been proven to be effective in improving self-management behaviour of patients with MetS components (i.e., diabetes or hypertension). However, evidence is lacking in terms of their effectiveness specifically for patients with MetS. The aim of this pilot study is to evaluate the feasibility and potential effectiveness of the EMPOWER-SUSTAIN Self-Management e-Health Intervention in improving activation and self-management behaviours among patients with MetS. This paper presents the study protocol. METHODS: A pilot randomised controlled trial will be conducted in a university primary care clinic. A total of 232 patients aged 18-60 years with MetS will be recruited; 116 will be randomised to receive the EMPOWER-SUSTAIN intervention for 6 months, and another 116 patients will continue with usual care. The EMPOWER-SUSTAIN intervention is a multifaceted chronic disease management strategy based on the Chronic Care Model and persuasive technology theory. It consists of training primary care physicians, nurses and patients to use the EMPOWER-SUSTAIN web-based self-management mobile app, strengthening the patient-physician relationship and reinforcing the use of relevant clinical practice guidelines to guide management and prescribing. The primary outcome is the mean change in patient activation score using the Patient Activation Measure short form Malay version (PAM-13-M) questionnaire. The secondary outcomes include the changes in waist circumference, body mass index, blood pressure, patient physical activity level, eating behaviour, perception of chronic illness care, satisfaction with patient-physician interaction, and perceived absolute 10-year cardiovascular disease risk. Feasibility of implementing the intervention will be evaluated. This includes acceptability of the intervention, estimating the likely rate of participant recruitment and retention, appropriateness of the outcome measures, calculation of sample size, and the intervention's potential effectiveness. CONCLUSION: To our knowledge, this is the first study in Malaysia that aims to determine the feasibility of a multifaceted e-health intervention, as well as to indicate more useful aspects of this intervention for further exploration in a larger trial. TRIAL REGISTRATION: ClinicalTrials.gov, NCT04120779. Registered on 9 October 2019, protocol version 1.