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The COVID-19 pandemic has left a deep mark on healthcare systems and society worldwide. In this context, the project “European Cohorts of Patients and Schools to Advance Response to Epidemics” (EuCARE), responding to an emergency request from the European Union under the Horizon Europe programme, addressed the pandemic from different perspectives. It investigated the clinical impact of emerging SARS-CoV-2 variants, the performance of vaccines and diagnostics, post-acute sequelae of SARS-CoV-2 infection (PASC), schooling and vaccine hesitancy. This short report combines a review of project outputs with a consultation of the ten project principal investigators and work package leaders, all of whom responded; no formal qualitative analysis was applied. The primary objective was to identify the operational and methodological challenges encountered during EuCARE and to explore their implications for the design and implementation of future pandemic research. Investigators reported four challenges requiring coordinated action at national and European level: fragmented ethics and regulatory procedures; difficulty in rapidly mobilising specialised personnel; vaccine hesitancy and other aspects of behavioural preparedness; and vulnerable diagnostic supply chains. From these experiences we derived six ''pills of preparedness'': evidence-based science, workforce surge capacity, data collection and management, specialised professional roles, collaborative networks, and evidence-based communication. These lessons derive from a single consortium and from the self-reported experience of a limited number of investigators, and should be interpreted accordingly.