The COVID-19 pandemic has had a significant impact on how field-based research is being conducted globally. Given the challenges of undertaking fieldwork during epidemics and the need for mixed methods research to address the social, political, and economic issues related to epidemics, there is a small but growing body of evidence in this area. To contribute to the logistical and ethical considerations for conducting research during a pandemic, we draw on the challenges and lessons learnt from adapting methods for two research studies conducted in 2021 during the COVID-19 pandemic in low- and middle-income country (LMIC) settings: (1) in-person research in Uganda and (2) combined remote and in-person research in South and Southeast Asia. Our case studies focus on data collection and demonstrate the feasibility of conducting mixed methods research, even with many logistical and operational constraints. Social science research is often used to identify the context of specific issues, to provide a needs assessment, or inform longer-term planning; however, these case studies have shown the need to integrate social science research from the start of a health emergency and in a systematic way. Social science research during future health emergencies can also inform public health responses during the emergency. It is also crucial to collect social science data after health emergencies to inform future pandemic preparedness. Finally, researchers need to continue research on other public health issues that are ongoing even during a public health emergency.