BackgroundThe specific palliative care needs and problems of patients with a substance use disorder and multiple problems, and those of their proxies, are under recognized Besides, the organization of palliative care, including the division of health care professionals’ responsibilities, is often unclear. Perspectives of patients and proxies are hardly known. We describe the outline of a study designed to explore how palliative care for patients with a substance use disorder is organized in the Netherlands and to explore problems and needs, as well as possible improvements from the healthcare professionals’, patients’ and proxies’ perspective. The aim of this protocol paper is to provide insights in ways to conduct research with vulnerable research participants and to offer a detailed description of the study design. The broader study aims to gain insight in and formulate recommendations on how to improve palliative care for patients with a substance use disorder.MethodsA qualitative study with patients, proxies and healthcare professionals. Semi-structured interviews will be held with 10–15 patients who suffer from a severe substance use disorder. They are in a palliative care trajectory and either diagnosed with a chronic or life-threatening disease or, as a result of addictive behavior, a physical deterioration without the prospect of cure. Semi-structured interviews will also be held with 5–10 proxies. Healthcare professionals, volunteers and/or ‘experts-by-experience’ (n = 24–40) will be participating in semi-structured group interviews. All (group) interviews will be thematically analyzed. Additionally, a strengths, weaknesses, opportunities and threats (SWOT) analysis will be applied to the group interview data with the aim to summarize and concretize the findings.DiscussionEveryone has a right to an optimal end-of-life phase of life and a dignified dying process. This study will provide valuable knowledge about palliative care for patients with a substance use disorder and explicitly bring to light the needs and problems of the patients and their proxies and healthcare professionals in a palliative care phase.Electronic supplementary materialThe online version of this article (10.1186/s12904-018-0351-z) contains supplementary material, which is available to authorized users.