Despite most Indonesian women now receiving antenatal care on the nationally recommended four occasions and being delivered by skilled birth attendants, the nation's maternal mortality ratio (MMR) is estimated as 177 per 100,000 live births. Recent research in a rural district of Indonesia has indicated that poor service quality due to organizational and personnel factors is now a major determinant of this high MMR. The present research is an in-depth analysis of possible health service organizational and quality of care related causes of death among 30 women admitted to a peak referral hospital in a major Indonesian city. Despite their condition being complex or deteriorating, most of these women arrived at the hospital in a state where it was feasible to prevent death with good quality care. Poor application of protocols, poor information flow from frontline hospitals to the peak referral hospital, delays in emergency care, and delays in management of deteriorating patients were the main contributing factors to these deaths. Pyramidal referrals also contributed, as many women were initially referred to hospitals where their condition could not be effectively managed. While generic quality improvement measures, particularly training and monitoring for rigorous application of clinical protocols (including forward planning for deteriorating patients) will help improve the situation, the districts and hospitals need to develop capacity to assess their local situation. Unless local organisational factors, staff knowledge and skill, blood and blood product availability, and local reasons for delays in providing care are identified, it may not be possible to effectively reduce the adverse pregnancy outcomes.