Background The public health crises that emerged in the COVID-19 pandemic significantly impacted the provision of medical care and placed sudden restrictions on ongoing clinical research. Patient-facing clinical research confronted unique challenges in which recruitment and study protocols were halted and then adapted to meet safety procedures during the pandemic. Our study protocol included the use of a Lung Cancer Screening Decision Tool (LCSDecTool) in the context of a primary care visit and was considerably impacted by the pandemic. We describe our experience adapting a multi-site clinical trial of the LCSDecTool within the Department of Veterans Affairs Health Care System. We conducted a randomized controlled trial (RCT) comparing the LCSDecTool to a control intervention. Outcomes included lung cancer screening (LCS) knowledge, shared decision-making, and uptake and adherence to LCS protocol. We identified three strategies that led to the successful adaptation of the study design during the pandemic: (1) multi-level coordination and communication across the organization and study sites, (2) flexibility and adaptability in research during a time of uncertainty and changes in regulation, and (3) leveraging technology to deliver the intervention and conduct study visits, which raised issues concerning equity and internal and external validity. Conclusion Our experience highlights strategies successfully employed to adapt an intervention and behavioral research study protocol during the COVID-19 pandemic. This experience will inform clinical research moving forward both during and subsequent to the constraints placed on research and clinical care during the COVID-19 pandemic.