Background: Ever since the peak in the number of refugees arriving in Germany in 2015, existing health care structures have faced major challenges. The city of Cologne developed ad-hoc new structures: a separate department for refugee medicine was set up. In the context of this study, the actual gaps in the health care of refugees in the city of Cologne were examined. The study provides lessons learnt for the health care of refugees. Methods: The present study used an embedded mixed-methods approach using 20 semi-structured interviews and a database including 353 datasets with socio-demographic, health-related and resource-related information to cross-check the results of qualitative data. Results: The qualitative data revealed gaps in providing health care to refugees. These gaps were found concerning approving health care services and medical aids by the municipality, communication and cooperation between the actors in care of refugees, undersupplies in mental health care and addictive disorders as well as improper housing situations for vulnerable groups of refugees with mental health issues, psychiatric disorders or elderly persons. Quantitative data confirmed the gap in approving health care services and medical aids, whilst no valid statement could be made about communication and cooperation. Undersupplies for mental health issues were confirmed, the gap for treatment of addictive disorders shows a divergence within the database. Improper housing situations for mentally ill persons were reflected, for elderly persons this did not appear in data. Conclusion: Analysing the gaps can stimulate necessary changes to improve health services for refugees locally, while others are beyond the control of the local authority and require legislative and political action.