Abstract Background While Malawi has achieved success in reducing overall under-five mortality, reduction of neonatal mortality remains a persistent challenge. There has, therefore, been a push to strengthen the capacity for quality newborn care at district hospitals through the implementation of innovative neonatal technologies such as bubble continuous positive airway pressure (CPAP). This study investigates tertiary- versus secondary-level hospital differences in capacities for bubble CPAP use and implications for implementation policies. Methods A secondary analysis of interviews was conducted with 46 health workers at one tertiary hospital and three secondary hospitals in rural Southern Malawi. Grounded theory was utilized to explore the emerging themes according to health worker cadres (nurse, clinician, district health management) and facility level (tertiary- and secondary-level facilities), which were managed using NVivo 12 (QSR International, Melbourne, Australia). Results We identified frequent CPAP use and the availability of neonatal nurses, physicians, and reliable electricity as facilitators for CPAP use at the tertiary hospital. Barriers at the tertiary hospital included initiation eligibility disagreements between clinicians and nurses and insufficient availability of the CPAP machines. At secondary-level hospitals, the use was supported by decision-making and initiation by nurses, involving caretakers to assist in monitoring and reliable availability of CPAP machines. Bubble CPAP was hindered by unreliable electricity, staffing shortages and rotation policies, and poor systems of accountability. Conclusion While this study looked at the implementation of bubble CPAP in Malawi, the findings may be applicable for scaling up other novel neonatal technologies in low-resource settings. Implementation policies must consider staffing and management structures at different health services levels for effective scale-up.