Cognitive biases are systematic cognitive distortions, which can affect clinical reasoning. The aim of this study was to unravel the most common cognitive biases encountered in in the peculiar context of the COVID-19 pandemic. Case study research design. Primary care. Single centre (Division of General Internal Medicine, University Hospitals of Geneva, Geneva, Switzerland). A short survey was sent to all primary care providers (N = 169) taking care of hospitalised adult patients with COVID-19. Participants were asked to describe cases in which they felt that their clinical reasoning was “disrupted” because of the pandemic context. Seven case were sufficiently complete to be analysed. A qualitative analysis of the clinical cases was performed and a bias grid encompassing 17 well-known biases created. The clinical cases were analyzed to assess for the likelihood (highly likely, plausible, not likely) of the different biases for each case. The most common biases were: “anchoring bias”, “confirmation bias”, “availability bias”, and “cognitive dissonance”. The pandemic context is a breeding ground for the emergence of cognitive biases, which can influence clinical reasoning and lead to errors. Awareness of these cognitive mechanisms could potentially reduce biases and improve clinical reasoning. Moreover, the analysis of cognitive biases can offer an insight on the functioning of the clinical reasoning process in the midst of the pandemic crisis.