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BACKGROUND: During the COVID-19 pandemic, health system managers and policymakers were vital in shaping response strategies, allocating resources, and overseeing healthcare delivery. Despite this, limited research has examined their perspectives on the health system response to the crisis, especially in the Latin American context. This study addresses that gap by exploring the health system's response to this pandemic in Cochabamba, Bolivia, through the lens of these key stakeholders.

METHODS: We conducted a qualitative study using semi-structured interviews with 10 health system managers and policymakers responsible for the pandemic response. Reflexive thematic analysis guided the development and interpretation of the themes.

RESULTS: Our findings shed light on how the pandemic revealed and intensified pre-existing vulnerabilities within the health system sectors. Political instability and centralized decision-making delayed the response, increased public unrest, and hindered resource mobilization. Fragmented governance structures and inadequate coordination between the public and social security sectors further weakened the health system's capacity. Health services, already strained before the pandemic, faced critical shortages in personnel, equipment, and infrastructure. Stay-at-home regulations, short-term staffing policies, and financial barriers exacerbated staff attrition. However, innovations such as telemedicine and non-conventional healthcare strategies helped mitigate gaps in service delivery.

CONCLUSIONS: Our findings highlight governance weaknesses, human resource limitations, and structural fragmentation of service delivery, which constrained the Bolivian health system's ability to respond effectively to the pandemic. Addressing these challenges requires strengthening intersectoral coordination and communication, improving workforce sustainability, and investing in better future public health emergency preparation. Improving governance mechanisms, allocating resources equitably, and integrating service delivery could enhance the health system's resilience capacity.