Objectives Our study described how the WHO intra-action review (IAR) methodology was operationalised and customised in three Western Balkan countries and territories and the Republic of Moldova and analysed the common key findings to inform analyses of the lessons learnt from the pandemic response. Design We extracted data from the respective IAR reports and performed a qualitative thematic content analysis to identify common (between countries and territories) and cross-cutting (across the response pillars) themes on best practices, challenges and priority actions. The analysis involved three stages, namely: extraction of data, initial identification of emerging themes and review and definition of the themes. Setting IARs were conducted in the Republic of Moldova, Montenegro, Kosovo and the Republic of North Macedonia between December 2020 and November 2021. The IARs were conducted at different time points relative to the respective pandemic trajectories (14-day incidence rate ranging from 23 to 495 per 100 000). Results Case management was reviewed in all the IARs, while the infection prevention and control, surveillance and country-level coordination pillars were reviewed in three countries. The thematic content analysis identified four common and cross-cutting best practices, seven challenges and six priority recommendations. Recommendations included investing in sustainable human resources and technical capacities developed during the pandemic, providing continuous capacity-building and training (with regular simulation exercises), updating legislation, improving communication between healthcare providers at all levels of healthcare and enhancing digitalisation of health information systems. Conclusions The IARs provided an opportunity for continuous collective reflection and learning with multisectoral engagement. They also offered an opportunity to review public health emergency preparedness and response functions in general, thereby contributing to generic health systems strengthening and resilience beyond COVID-19. However, success in strengthening the response and preparedness requires leadership and resource allocation, prioritisation and commitment by the countries and territories themselves.