In recent years, medical sociology has produced a significant amount of publications about the effects of the COVID-19 pandemic on medical care provision and healthcare professionalism around the globe. This study builds on this line of research by looking at a rarely discussed case of pandemic management—the case of Russia’s centralized and state-dominated medical sector. In our analysis, we focus on the organizational level and the institutional work of front-line health professionals. Using a neoinstitutional theoretical lens, we show how, as a result of the conflict between professional and managerial logics, pockets of extreme institutional uncertainty emerged within Russian healthcare: “non-COVID” healthcare facilities and hospitals rapidly restructured for COVID-19 care. Qualitative interviews with healthcare professionals indicate that institutional misalignment inside these “gray zones” translated into the material dimension, significantly impeding the effectiveness of the pandemic response. While sociological literature frequently portrays Russian health professionals as fully subjected to administrative constraints and disempowered, our data allows us to trace their informal institutional work and agency during the health crisis. Through these materially mediated work, our informants attempted to deal with both the challenges of the pandemic and institutional contradictions of the Russian healthcare system. Professionals’ institutional work brought some improvements to Russia’s pandemic-affected clinical settings. However, being informal and purposefully hidden, it neither constituted a viable solution for medical organizations, nor contributed to the strengthening of professionals’ autonomy.