Institutional quarantine was one of the key public health measures used to control the spread of the COVID-19. Institutional quarantine has been associated with several psychosocial and economic risks to affected individuals. However, little is known about the psychosocial and economic risks it poses to affected persons in low-resource countries, since it is a relatively new strategy for controlling disease spread in these settings. This article provides insights into the economic and psychosocial risks encountered by affected persons in a low-resource context. We conducted narrative interviews with 20 adults placed under institutional quarantine to contain the COVID-19 pandemic in Uganda. Institutional quarantine exposed affected persons to an intricate range of economic and psychosocial risks including loss of livelihoods and/or income, financial distress, fear, worry, anger, loneliness and stigma. The experience of specific risks was shaped by an intersection of individual and contextual factors. However, disregard for economic and social issues and shortcomings in the implementation of institutional quarantine contributed profoundly to the occurrence of risks. Integration of measures for identification and continuous management of the broad range of potential risks to individuals and bridging gaps in the implementation of institutional quarantine, may help to minimise associated economic and psychosocial risks.