© 2021, The Author(s).Background: Turkey hosts nearly four million refugees and 99% live in urban areas. Research in urban settings pose different challenges and opportunities than research in refugee camps. In this article, we aimed to share the challenges and experiences we encountered in a mixed-methods study to assess mental health problems and barriers to accessing mental health care among refugees in urban areas of Turkey. Discussion: In our case, the main challenges in conducting research with refugees were collecting data from a highly traumatized population, difficulties with contacting undocumented asylum seekers including trust issues and the fear of deportation, the risk of secondary traumatization among data collectors, and the bureaucracy during study approval processes. Targeting a representative sample was not feasible, because of the lack of publicly available demographic data on a district level, presence of undocumented asylum seekers and high mobility among the refugees. Although respondents with significant psychological symptoms were routinely referred to available mental health services, we were able to do less for unregistered refugees with problems in accessing health care. Language/alphabet differences and differing dialects of Arabic posed another challenge in both translation and administration of the scales. Based on cultural characteristics, a gender-balanced team was used and the interviewers were gender-matched whenever needed. Also, the research team had to work after work hours and during weekends to be able to interview male refugees, since most refugee men were at work during working hours and most days of the week. Conclusions: The research team’s experience showed that refugee population characteristics including level of trauma, language, culture, gender, legal status, and urban setting characteristics including places of living, mobility, availability of publicly available demographic data, and outreach-related barriers lead to different challenges and ethical responsibilities of researchers and affect the research costs in terms of time, human resources and finance. Even in a host country with geographical, religious and cultural proximity to the refugees, profound challenges exist in conducting mental health research in urban settings. Learning from previous experience and collaborating with local researchers and institutions are vital for better public health research and practice outcomes.