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Introduction 4 years after the Ebola outbreak, the arrival of COVID-19 presented West Africa with a new shock. Despite widespread disruptions, malaria service continuity remained a priority in both countries. In Sierra Leone, the proportion of pregnant women receiving at least three doses of intermittent preventive treatment increased from 36% in 2018 to 50% in 2021. Similarly, insecticide-treated net ownership in Guinea rose from 44% to 63%, reflecting the ability of national programmes to sustain essential interventions despite pandemic-related constraints. Against this backdrop, this study investigates the strategies used to strengthen health system resilience in Guinea and Sierra Leone during the pandemic. Specifically, it explores how both countries responded to the pandemic’s demands and mitigated potential negative effects on health service delivery, using malaria as an example of routine care.Methods We conducted a document review and interviewed 36 key informants (16 in Guinea and 20 in Sierra Leone) leading malaria elimination efforts and the national COVID-19 response. The review included malaria surveillance data and health performance reports to contextualise our qualitative findings. Interviews identified strategic responses by decision-makers overseeing malaria and COVID-19 efforts. This qualitative approach offers an in-depth understanding of decision-making within broader health systems.Results Three major themes were shared between countries: (1) ‘Responding quickly and decisively to COVID-19’, (2) ‘Ensuring continuity of essential services during the pandemic’ and (3) ‘Improving health system responsiveness, despite contextual challenges’. The document review confirmed sustained malaria service delivery, with minimal declines in outpatient consultations compared to Ebola.Conclusions Strategies used in both countries enabled the health systems to absorb the acute shock of COVID-19, adapt to the challenges and transform aspects to improve responsiveness. Institutionalising these policies and fostering agility could enhance pandemic preparedness and contribute to stronger health systems in these and other low-income countries in the region.