The COVID-19 pandemic has disrupted global supply chains and caused widespread shortages of healthcare supplies. This mixed-methods study examined the management of supply shortages in Swedish hospitals during the COVID-19 pandemic. The key findings are that the shortage of supplies was initially severe owing to low regional and national contingency inventory levels, a lack of knowledge of supply chain management, and cost-saving measures. The perceived consequences of the shortage of personal protective equipment persisted in emergency and inpatient departments, in the later waves. Although pharmaceutical shortages later decreased, hospital managers were disappointed that they persisted. This study also highlights the effectiveness of consensus-based hourly supply agreements between service organisations and unit managers, which makes the prioritisation of the limited supply more dynamic. Despite these challenges, hospitals were able to adapt to the supply chain disruptions caused by the pandemic; however, the results emphasise the importance of preparedness for future pandemics.