IntroductionUganda has high maternal, neonatal, and under-five mortality rates. This study documents stakeholder perspectives on best practices in a maternal and newborn health (MNH) quality-improvement programme implemented in the West Nile region of Uganda to improve delivery and utilisation of MNH services.MethodsThis exploratory cross-sectional qualitative study, conducted at the end of 2021, captured the perspectives of stakeholders representing the different levels of the healthcare system. Data were collected in four districts through: interviews with key informants working at all levels of the health system; focus group discussions with parents and caretakers and with community health workers; and interviews with individual community members whose lives had been impacted by the MNH programme. The initial content analysis was followed by a deductive synthesis pitched according to the different levels of the health system and the health-systems building blocks.ResultsThe findings are summarised according to the health-systems building blocks and an account is given of three of the interventions most valued by participants: (1) data use for evidence-based decision making (with regard to human resources, essential reproductive health commodities, and financing); (2) establishment of special newborn care units and high-dependency maternity units at district hospitals and training of the health workforce (also with reference to other infrastructural improvements such as the provision of water, sanitation and hygiene facilities at health facilities); and (3) community referral of pregnant women through a commercial motorcycle voucher referral system.ConclusionThe MNH programme in the West Nile region adopted a holistic and system-wide approach to addressing the key bottlenecks in the planning, delivery, and monitoring of quality MNH services. There was general stakeholder appreciation across the board that the interventions had the potential to improve quality of care and newborn and maternal health outcomes. However, as the funding was largely donor-driven, questions about government ownership and sustainability in the context of limited resources remain.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12913-023-09480-x.