There are global calls for research to support health system strengthening in low-income and middle-income countries (LMICs). To examine the nature and magnitude of gaps in access and quality of inpatient neonatal care provided to a largely poor urban population, we combined multiple epidemiological and health services methodologies. Conducting this work and generating findings was made possible through extensive formal and informal stakeholder engagement linked to flexibility in the research approach while keeping overall goals in mind. We learnt that 45% of sick newborns requiring hospital care in Nairobi probably do not access a suitable facility and that public hospitals provide 70% of care accessed with private sector care either poor quality or very expensive. Direct observations of care and ethnographic work show that critical nursing workforce shortages prevent delivery of high-quality care in high volume, low-cost facilities and likely threaten patient safety and nurses' well-being. In these challenging settings, routines and norms have evolved as collective coping strategies so health professionals maintain some sense of achievement in the face of impossible demands. Thus, the health system sustains a functional veneer that belies the stresses undermining quality, compassionate care. No one intervention will dramatically reduce neonatal mortality in this urban setting. In the short term, a substantial increase in the number of health workers, especially nurses, is required. This must be combined with longer term investment to address coverage gaps through redesign of services around functional tiers with improved information systems that support effective governance of public, private and not-for-profit sectors.