IntroductionHealth information systems represent an opportunity to improve the care provided to people with multimorbidity. There is a pressing need to assess their impact on clinical outcomes to validate this intervention. Our study will determine whether using a digital platform (Multimorbidity Management Health Information System, METHIS) to manage multimorbidity improves health-related quality of life (HR-QoL).Methods and analysisA superiority, cluster randomised trial will be conducted at primary healthcare practices (1:1 allocation ratio). All public practices in the Lisbon and Tagus Valley (LVT) Region, Portugal, not involved in a previous pilot trial, will be eligible. At the participant level, eligible patients will be people with complex multimorbidity, aged 50 years or older, with access to an internet connection and a communication technology device. Participants who cannot sign/read/write and who do not have access to an email account will not be included in the study. The intervention combines a training programme and a customised information system (METHIS). Both are designed to help clinicians adopt a goal-oriented care model approach and to encourage patients and carers to play a more active role in autonomous healthcare. The primary outcome is HR-QoL, measured at 12 months with the physical component scale of the 12-item Short Form questionnaire (SF-12). Secondary outcomes will also be measured at 12 months and include mental health (mental component Scale SF-12, Hospital Anxiety and Depression Scale). We will also assess serious adverse events during the trial, including hospitalisation and emergency services. Finally, at 18 months, we will ask the general practitioners for any potentially missed diagnoses.Ethics and disseminationThe Research and Ethics Committee (LVT Region) approved the trial protocol. Clinicians and patients will sign an informed consent. A data management officer will handle all data, and the publication of several scientific papers and presentations at relevant conferences/workshops is envisaged.Trial registration numberNCT05593835.