This study addresses the risk and vulnerability of Chilean salmon production to hazards resulting from the COVID-19 pandemic threat, including limited access to farms, limited processing capacity and reduced market demand. The role of different management approaches in reducing risk and vulnerability is also explored. Results suggest that concession areas having the largest accumulated and current biomass have the highest risk, which is also transferred to the municipal level. The scenarios modelled with better management practices that reduce diseases were able to reduce risks by 30–40%. The largest risk reduction is achieved when production biomass is divided in a more equitable manner among concession areas, suggesting the need for strategic improvements in spatial planning of the activity in the marine environment according to ecosystem carrying capacity and better practices. Improving adaptation capacity can reduce vulnerability between 20% and 30% for municipalities; for example, providing local employment can be a win-win management measure under the COVID-19 threat because it reduces movement of people and facilitates handling and responses to emergencies. A larger footprint in local economies and employment can also improve social perception and acceptance of the sector, thus contributing to improve adaptation changes and governance to face the threats. The framework used here to perform a risk and vulnerability assessment of salmon farming to the pandemic-associated threats can also be useful for other aquaculture systems elsewhere, provided that relevant information is available.