Elevated rates of mental health difficulties are frequently reported in conflict-affected and displaced populations. Even with advances in improving the validity and reliability of measures, our knowledge of the performance of assessment tools is often limited by a lack of contextualization to specific populations and socio-political settings. This reflective paper aimed to review challenges and share lessons learned from the process of administration and supervision of a structured clinical interview, the MINI International Neuropsychiatric Interview for Children and Adolescents (MINI Kid) and the Clinical Global Impression (CGI) severity scale, with N=119 Syrian refugee children (aged 8-17) resident in informal tented settlements in Lebanon. Qualitative data was derived from supervision process notes on challenges that arose during assessments, analyzed for thematic content. Five themes were identified: 1) practical and logistical challenges (changeable nature of daily life, competing demands, access to phones, temporary locations, limited referral options); 2) validity (lack of privacy, trust, perceptions of mental health, stigma, false positive answers); 3) cultural norms and meaning (impact of different meanings on answers); 4) contextual norms (reactive and adaptive emotional and behavioral responses to contextual stress); and 5) co-morbidity and formulation (interconnected and complex presentations). The findings suggest that while structured assessments have major advantages, cultural and contextual sensitivity during assessments, addressing practical barriers to improve accessibility, and consideration for inter-connected formulations is essential to help inform prevalence rates, treatment plans, and public health strategies.