In Malawi, it has been observed that some women are dying even when they reach a comprehensive emergency obstetric care facility where the quality is expected to be high and the maternal mortality low. The objective of this study was to describe shortcomings within the maternal healthcare delivery system that might have contributed to maternal deaths in the district of Lilongwe. Retrospectively, 14 maternal deaths that occurred between January 1, 2011 and June 30, 2011 were reviewed. Interviews were conducted with healthcare workers who provided care to the deceased women. Triangulated data from the respective medical charts and interview transcripts were analyzed using a directed approach to content analysis. Excerpts were categorized according to three main components of the maternal healthcare delivery system: skill birth attendant (SBA), enabling environment (EE) and referral system (RS). Most of the shortcomings identified were grouped under SBA. They included inadequate clinical workups and monitoring, missed and incorrect diagnoses, delayed or incorrect treatment, delayed referrals and transfers, patients not being stabilized before being referred and outright negligence. The SBA component should be investigated further. Interventions based on evidence from these investigations may have a positive impact on maternal mortality.