Existing empirical work has analysed the impacts of COVID-19 on mortality, fertility and international migration. Less is known about the ways in which the COVID-19 pandemic has influenced the patterns of internal migration. Anecdotal reports of mass migration from large cities to less populated areas have emerged but lack of data has prevented empirically assessing this hypothesis. Drawing on geographically granular administrative population register data, we aim to analyse the extent of change in the patterns of internal migration across the urban hierarchy in Spain during 2020. Our results show a decline of 2.5% in the number of internal migration moves, particularly during the early stages of the pandemic, returning to pre-pandemic levels in late 2020. Results also reveal unusually large net migration losses in core cities and net migration gains in rural areas. Net migration losses in cities and gains in rural areas particularly accumulated following the easing of some non-pharmaceutical interventions. Yet, these net losses and gains trended to pre-pandemic levels in late 2020, and movements between cities, and between cities and suburbs, continued to dominate the internal migration system. Thus, while the COVID-19 pandemic exerted notable changes in the geographic balance of internal migration flows, these changes appear to have been temporary and did not significantly alter the existing structures of the national migration system