In the wake of several infectious disease outbreaks during the past two decades – including COVID-19 and Ebola - there has been increasing use of alternative clinical trial designs (such as adaptive trials) in public health emergency contexts. The use of these research models, predominantly conducted through international partnership between two or more research institutions, has accelerated identification of important aspects of disease transmission, prevention, and treatment that directly impact both global clinical knowledge and local public health policy. However, these methods and partnership models also introduce novel ethical questions around their design and use, particularly within the context of limited-resource settings. In this project, we conceptualized the ethical considerations around use of alternative clinical trial designs during public health emergencies with a focus on fair and inclusive research practices within complex international research partnerships in resource-limited settings. A deliberative process was used to identify and categorize themes into a conceptual model that critically analyzes the ethical tensions between scientific knowledge production, protection of research participants, and research-related obligations to the community during a public health emergency. We address issues including informed consent, clinical equipoise, obligations to local research capacity and ethical oversight, and the use alternative clinical trial research protocols within partnerships that have discordant financial and material resources. Identifying key ethical questions and challenges to fair and inclusive research practices within the context of alternative clinical trials is an important step to ensure better preparedness for ongoing and future public health emergencies in resource-limited settings.