Self-isolation and quarantine have become a key part of New Zealand’s border controls and containment strategy against COVID-19. However, we have very little information on public understanding of these measures and adherence with these critical interventions. There are also likely to be ethnic and socioeconomic inequalities in the ability of people to follow these guidelines. This research will use mixed-methods to provide a comprehensive picture of the operation of isolation measures in NZ, including: a population-based sample of people registered with Healthline for self-isolation to assess knowledge, attitudes and practices regarding isolation measures. This research addresses critical knowledge gaps by identifying actions taken, and factors influencing individuals’ understanding of and ability to comply with advice to self-isolate. Findings will be fed back rapidly to the MoH to support immediate improvements in how self-isolation is managed.