The global dynamics of seasonal influenza viruses inform the design of surveillance, intervention, and vaccination strategies. The COVID-19 pandemic provided a singular opportunity to evaluate how influenza circulation worldwide was perturbed by human behavioral changes. We combine molecular, epidemiological, and international travel data and find that the pandemics onset led to a shift in the intensity and structure of international influenza lineage movement. During the pandemic, South Asia played an important role as a phylogenetic trunk location of influenza A viruses, whereas West Asia maintained the circulation of influenza B/Victoria. We explore drivers of influenza lineage dynamics across the pandemic period and reasons for the possible extinction of the B/Yamagata lineage. After a period of 3 years, the intensity of among-region influenza lineage movements returned to pre-pandemic levels, with the exception of B/Yamagata, after the recovery of global air traffic, highlighting the robustness of global lineage dispersal patterns to substantial perturbation.