ObjectiveAlthough the caesarean delivery (CD) rate has substantially increased, little is known about its impacts when performed in the first and second stages of labour on fetomaternal outcomes, especially among referred mothers. Thus, this study aimed to investigate the association between CDs performed during the first and second stages of labour and poor maternal and neonatal outcomes among mothers referred to tertiary centres.SettingThis retrospective cohort study analysed medical records of mother–infant pairs from September 2020 to May 2023 in Southern Ethiopia.ParticipantsWe retrospectively collected data from 848 participants who underwent emergency CD on a referral basis during the study period.Primary outcome measureThe primary outcomes of interest were adverse maternal and neonatal outcomes. Data were analysed using descriptive and inferential statistics.ResultsOf the 848 CDs, 722 (85.2%) and 126 (14.8%) were performed at the first and second stages of labour, respectively. Caesarean sections performed at the second stage were higher with nulliparity, increased maternal age, and birth weight. Compared with the first-stage CD, the second-stage CD was associated with a significantly increased risk of adverse maternal (OR 3.7, 95% CI 2.4 to 5.7) and neonatal outcomes (OR 2.0; 95% CI 1.3 to 2.9), including neonatal death.ConclusionSecond-stage CDs have an increased risk of adverse maternal and neonatal outcomes. Strengthening and improving obstetric emergency surgical services and intensive neonatal care for those populations would help decrease the maternal and fetal negative consequences.