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(1) Background. During the COVID-19 pandemic, healthcare professionals faced psychological and social challenges in addition to a sharp increase in workload. The aim of this work was to reveal how healthcare and pharmacy workers assessed their wellbeing and the methods of coping they employed to overcome stress during quarantine. (2) Methods. The mixed-method study was conducted between August and October 2020, integrating quantitative (n = 967) and qualitative (n = 27) strategies. Doctors, nurses, healthcare administrative staff, pharmacy specialists, and other employees of the healthcare system were interviewed retrospectively about their experiences during and following lockdown (March–June 2020). (3) Results. Overall, 38.7% of the respondents reported a decrease in psychological wellbeing, while 23.4% of the respondents reported a decrease in physical wellbeing during quarantine. The healthcare professionals’ narratives identified a shift from nonspecific fears at the beginning of the pandemic to the more concrete fear of contracting COVID-19, of infecting others, and about their loved ones, as well as undifferentiated fear. Multivariate analysis revealed that a subjective decrease in wellbeing was typical in professionals who had had direct contact with patients infected with COVID-19, as well as those with stronger fears, and those who were more likely to employ compulsive distancing and substance use as ways to cope with stress. (3) Conclusions. The results suggest that lockdown had a negative impact on healthcare workers’ wellbeing during the first pandemic wave in 2020.