Conflict-affected women and girls living in protracted forced displacement settings are vulnerable to sexually transmitted infections (STIs). Yet, little is known about the risk factors for and lived experiences of STIs in complex humanitarian settings, particularly in the Middle East and North Africa, where STIs have long been understudied. This qualitative study adapts the social ecological model to characterize the multi-level risks for and lived experiences of STIs among Syrian refugee women resettled in an urban refugee camp in Beirut, Lebanon. Adopting a community-based sampling strategy, community health workers, who were refugee women from the camp, recruited and conducted in-depth interviews (IDIs) with 30 adult Syrian refugee women. Data were analyzed using an interpretative phenomenological approach and thematically organized according to the levels of the social ecological model. We identified a confluence of individual, interpersonal, community-based, and societal vulnerabilities to STIs, including extreme poverty and insecurity, patriarchal gender norms, stigma, sexual exploitation and trafficking, poor healthcare accessibility, intimate partner violence, including marital rape, transactional sex, sexual harassment, social isolation, and internalized stigma. Participants described experiencing bothersome symptoms and sequelae of advanced and untreated STIs in the setting of limited access to health services and challenges with engaging their partners in STI treatment, largely due to STI stigma. These novel findings suggest dynamic, interrelated social and health disparities across all social ecological levels influencing refugee women’s sexual health, including their risk of STIs. Comprehensive, multi-sectorial interventions, which transcend traditional public health methods and which adopt a sexual well-being approach, are urgently needed to address systemic and intrapersonal violence against refugee women, examine and mitigate the burden of STIs, and ensure sexual justice and health equity in this protracted forced displacement setting.