The power afforded to the administrative state is heavily reliant on public trust and the perception of evidence-based agency decision-making. Organizational reputation is key to preserving regulatory power. However, recent investigations reveal that existing scientific integrity policies may not be sufficient to preserve the credibility of many federal agencies. In fact, a significant number of career scientists across various entities – including the FDA – have observed unreported incidents of political interference. While political influence exerted by the executive branch to set policy goals and determine agency priorities can be beneficial, political pressures must not undermine public trust in scientific agencies. Recently, public perception regarding the FDA’s COVID-19 response threatened to weaken the agency’s longstanding reputation as the gold standard of review. The COVID-19 pandemic publicized vulnerabilities that exist across agencies, as well as those that are unique to the FDA. The FDA’s evolution as an increasingly public health-focused agency that must function in the landscape of politicized science exposes the agency to a greater risk of political interference. After all, the FDA’s involvement in public health requires increased participation in non-ideal, value-based decision-making. Throughout its history, the FDA has managed to maintain its reputation through its firm responses to scandal. The COVID-19 pandemic provides a platform for the FDA to – once again – look introspectively and institute safeguards addressing vulnerabilities that plagued the agency’s pandemic response. This Article examines the FDA’s early COVID-19 response to propose reforms that promote meaningful transparency, public accountability, and scientific integrity.