HIV-positive refugees confront a variety of challenges in accessing and adhering to antiretroviral therapy (ART) and attaining durable viral suppression; however, there is little understanding of what these challenges are, how they are navigated, or how they may differ across humanitarian settings. We sought to document and examine accounts of the threats, barriers and facilitators experienced in relation to HIV treatment and care and to conduct comparisons across settings. We conducted semi-structured interviews among a purposive sample of 14 refugees attending a public, urban HIV clinic in Kuala Lumpur, Malaysia (July-September 2010), and 12 refugees attending a camp-based HIV clinic in Kakuma, Kenya (February-March 2011). We used framework methods and between-case comparison to analyze and interpret the data, identifying social and environmental factors that influenced adherence. The multiple issues that threatened adherence to antiretroviral therapy or precipitated actual adherence lapses clustered into three themes: "migration", "insecurity", and "resilience". The migration theme included issues related to crossing borders and integrating into treatment systems upon arrival in a host country. Challenges related to crossing borders were reported in both settings, but threats pertaining to integration into, and navigation of, a new health system were exclusive to the Malaysian setting. The insecurity theme included food insecurity, which was most commonly reported in the Kenyan setting; health systems insecurity, reported in both settings; and emotional insecurity, which was most common in the Kenyan setting. Resilient processes were reported in both settings. We drew on the concept of "bounded agency" to argue that, despite evidence of personal and community resilience, these processes were sometimes insufficient for overcoming social and environmental barriers to adherence. In general, interventions might aim to bolster individuals' range of action with targeted support that bolsters resilient processes. Specific interventions are needed to address locally-based food and health system insecurities.