ObjectivesImplementation research was employed to examine rates and contextual factors associated with mothers’ care-seeking for their sick neonates and identify challenges for community-based possible serious bacterial infection (PSBI) services access and implementation during the COVID-19 pandemic.DesignWe conducted formative research involving household survey and programmatic qualitative study.SettingThis formative study was conducted in Dembecha and Lume woredas of Amhara and Oromia regions.ParticipantsData were captured from 4262 mothers aged 15–49 years who gave live birth 2–14 months before data collection, and interviews with 18 programme managers and 16 service providers in April to May 2021.AnalysisA multilevel regression model was employed to identify predictors of maternal care-seeking for PSBI and thematic qualitative analysis to inform strategy development to strengthen PSBI implementation.ResultsOverall, 12% (95% CI 11.0% to 12.9%) and 8% (95% CI 7.9% to 9.6%) of mothers reported any newborn illness and severe neonatal infection (PSBI), respectively. More than half of mothers sought formal medical care, 56% (95% CI 50.7% to 60.8%) for PSBI. Women who received postnatal care within 6 weeks (adjusted OR (AOR) 2.08; 95% CI 1.12 to 3.87) and complete antenatal care (ie, weight measured, blood pressure taken, urine and blood tested) (AOR 2.04; 95% CI 1.12 to 3.75) had higher odds of care-seeking for PSBI. Conversely, fear of COVID-19 (AOR 0.27; 95% CI 0.15 to 0.47) and residing more than 2 hours of walking distance from the health centre (AOR 0.39; 95% CI 0.16 to 0.93) were negatively associated with care-seeking for severe newborn infection. Multiple pre-existing health system bottlenecks were identified from interviews as barriers to PSBI service delivery and exacerbated by the COVID-19 pandemic.ConclusionWe found gaps in and factors associated with care-seeking behaviour of mothers for their sick young infants including fear of COVID-19 and pre-existing health system-level barriers. The findings of the study were used to design and implement strategies to mitigate COVID-19 impacts on management of PSBI.