Introduction Optimal medication management is one of the basic conditions necessary for home-dwelling older adults living with multiple chronic conditions (OAMCC) to be able to remain at home and preserve their quality of life. Currently, the reasons for such high numbers of emergency department visits and the very significant rate of hospitalisations for OAMCC, due to medication-related problems (MRPs), is poorly explored. This study aims to reveal the current state of the medication management practices of polymedicated, home-dwelling OAMCC and to make proposals for improving clinical and medication pathways through an innovative and integrated model for supporting medication management and preventing adverse health outcomes. Methods and analysis A mixed-methods study will address the medication management of polymedicated, home-dwelling OAMCC. Its explanatory sequential design will involve two major phases conducted sequentially over time. The quantitative phase will consist of retrospectively exploiting the last 5 years of electronic patient records from a local hospital (N ≈ 50 000) in order to identify the different profiles—made up of patient-related, medication-related and environment-related factors—of the polymedicated, home-dwelling OAMCC at risk of hospitalisation, emergency department visits, hospital readmission (notably for MRPs), institutionalisation or early death. The qualitative study will involve: (a) obtaining and understanding the medication management practices and experiences of the identified profiles extracted from the hospital data of OAMCC who will be interviewed at home (N ≈ 30); (b) collecting and analysing the perspectives of the formal and informal caregivers involved in medication management at home in order to cross-reference perspectives about this important dimension of care at home. Finally, the mixed-methods findings will enable the development of an innovative, integrated model of medication management based on the Agency for Clinical Innovation framework and Bodenheimer and Sinsky’s quadruple aim. Ethics and dissemination Ethical approval has been obtained from the Human Research Ethics Committee of the Canton Vaud (2018-02196). Findings will be disseminated in peer-reviewed journals, professional conferences and other knowledge transfer activities with primary healthcare providers, hospital care units, informal caregivers’ and patients’ associations.