BackgroundSepsis is a leading cause of neonatal mortality, despite the availability of effective treatment of possible serious bacterial illness (PSBI), including when referral to a hospital is not feasible. Gaps in access and delivery worsened during COVID-19. We conducted embedded implementation research in Ethiopia and Kenya aimed at mitigating the impact of COVID-19 and addressing various implementation challenges to improve PSBI management.MethodsThe implementation research projects were implemented at the subnational level in Ethiopia and Kenya between November 2020-June 2022 (Ethiopia) and December 2020-August 2022 (Kenya). Guided by the implementation research frameworks, both projects conducted mixed formative quantitative and exploratory research from April to May 2021, followed by summative evaluations conducted between June and July 2022. Frameworks encompassed Consolidated Framework for Implementation Research (CFIR), Reach, Effectiveness, Adoption, Implementation, and Maintenance (RE-AIM), as well as health systems framework that incorporates cascades of care and World Health Organization Health Systems Building Blocks. Results were synthesized across the projects through document review and sharing cross-project measures and strategies through a project community of practice.ResultsDespite differences in settings across the projects, cross-cutting facilitators included community health worker program and support, and existence of guidelines for PSBI management at primary care levels. Barriers included community attitudes towards seeking care for sick newborns, COVID-19 risks and fear, and lack of health care worker competence. Country-specific contextual barriers included supply chain issues, civil conflict (Ethiopia), and labor strikes (Kenya). Strategies chosen to mitigate barriers and support implementation and sustainability in both settings included leveraging community health workers to address resistance to care-seeking, health workers’ training, COVID-19 infection prevention measures, stakeholder engagement, and advocacy to integrate PSBI management into existing programs, policies, and training. Other strategies addressing emerging project-specific barriers, included improving follow-up through a community health desk and PSBI mobile app (Kenya) and supply chain strengthening (Ethiopia). Both projects improved PSBI management coverage, increased adoption and uptake, and informed national policy changes supporting potential for sustainability.ConclusionsPragmatic embedded implementation research effectively supports the identification of barriers and mapping to strategies designed to increase effective coverage of PSBI management when referral is not feasible during the COVID-19 pandemic. Despite differences in context, cross-cutting strategies identified could inform broader scale-up in the region, including during future health system shocks.