The COVID-19 crisis focused attention on how experts from different scientific fields provided advice to governments through expert committees and task forces. We compared experiences in two federal democracies, Belgium and Australia, by applying a mixed methods approach (literature review, media review, policy documents analysis). This comparative study found that expertise was institutionalized in different ways and its processes and priorities shifted over time. The policy coordination challenges inherent in federalism were largely overcome in Australia through strongly embedded health advisory processes. In Belgium, the advisory process was less stable, with advisory councils being abandoned, replaced, expanded, or downgraded during the course of the crisis.