Background: Homeless people experience multiple health problems and early mortality. In the Netherlands, they can get shelter-based end-of-life care, but shelters are predominantly focused on temporary accommodation and recovery. Aim: To examine the characteristics of homeless people who reside at the end-of-life in shelter-based nursing care settings and the challenges in the end-of-life care provided to them. Design: A retrospective record study using both quantitative and qualitative analysis methods. Setting/participants: Two Dutch shelter-based nursing care settings. We included 61 homeless patients who died between 2009 and 2016. Results: Most patients had somatic (98%), psychiatric (84%) and addiction problems (90%). For 75% of the patients, the end of life was recognised and documented; this occurred 0–1253 days before death. For 26%, a palliative care team was consulted in the year before death. In the three months before death, 45% had at least three transitions, mainly to hospitals. Sixty-five percent of the patients died in the shelter, 27% in a hospital and 3% in a hospice. A quarter of all patients were known to have died alone. Documented care difficulties concerned continuity of care, social and environmental safety, patient–professional communication and medical-pharmacological alleviation of suffering. Conclusions: End-of-life care for homeless persons residing in shelter-based nursing care settings is characterised and challenged by comorbidities, uncertain prognoses, complicated social circumstances and many transitions to other settings. Multilevel end-of-life care improvements, including increased interdisciplinary collaboration, are needed to reduce transitions and suffering of this vulnerable population at the end of life.