Abstract Background The reopening of schools during the COVID-19 pandemic has had a profound global impact, affecting millions of students, educators, and families worldwide. This organisation study, conducted in collaboration with professionals from Brazil, Mozambique, and Portugal, focuses on the organisation of school environments to ensure education safety and continuity, underscoring the global relevance of our findings. Methods A consortium of 12 countries developed a script for the semi-structured online interviews used in this study, which took place between March and December 2021. Focusing on the reorganisation of schools during lockdowns in the classroom, we interviewed 12 native Portuguese speakers involved in this process. We applied thematic analysis using NVivo v.22.0 to transcript interviews. Results Results revealed complexities in school reopening during the public health crisis. Key barriers were disparities between public and private schools and inadequate infrastructure. Facilitators included thorough preparation of staff, community engagement, and strong collaboration between the educational and health sectors, along with classroom and school space adaptations. Conclusions This study highlighted significant barriers and facilitating factors affecting school reopening during the pandemic. Challenges such as educational inequalities and infrastructure gaps were evident, while effective facilitation involved comprehensive planning and stakeholder engagement. These findings offer valuable insights for strategic planning and professional practice in ensuring safe and continuous education during pandemics. Key messages • Global collaboration in this study spotlights the complex challenges and necessary strategies for safely reopening schools amid a pandemic. • Research underscores the critical role of thorough preparation and community engagement in overcoming educational disparities during crises.