Background Provision of Emergency Obstetric and Neonatal Care (EmONC) reduces maternal mortality and should include three components: Basic Emergency Obstetric and Neonatal Care (BEmONC) offered at primary care level, Comprehensive EmONC (CEmONC) at secondary level and a good referral system in-between. In a conflict-affected province of Afghanistan (Khost), we assessed the performance of an Médecins Sans Frontières (MSF) run CEmONC hospital without a primary care and referral system. Performance was assessed in terms of hospital utilisation for obstetric emergencies and quality of obstetric care. Methods A cross-sectional study using routine programme data (2013–2014). Results Of 29,876 admissions, 99% were self-referred, 0.4% referred by traditional birth attendants and 0.3% by health facilities. Geographic origins involved clustering around the hospital vicinity and the provincial road axis. While there was a steady increase in hospital caseload, the number and proportion of women with Direct Obstetric Complications (DOC) progressively dropped from 21% to 8% over 2 years. Admissions for normal deliveries continuously increased. In-hospital maternal deaths were 0.03%, neonatal deaths 1% and DOC case-fatality rate 0.2% (all within acceptable limits). Conclusions Despite a high and ever increasing caseload, good quality Comprehensive EmONC could be offered in a conflict-affected setting in rural Afghanistan. However, the primary emergency role of the hospital is challenged by diversion of resources to normal deliveries that should happen at primary level. Strengthening Basic EmONC facilities and establishing an efficient referral system are essential to improve access for emergency cases and increase the potential impact on maternal mortality.