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The role of short-course antimicrobial prophylaxis (ScAP) after emergency caesarean section is unclear, particularly in low-middle-income countries. We aimed to address this knowledge gap by investigating its effectiveness and exploring the populations that might most benefit from post-delivery ScAP. We conducted a retrospective cohort study on women without signs or symptoms of any infection during admission for emergency caesarean section. The exposure was standard perioperative care (SPoC) or SPoC + ScAP. The standard ScAP included a 3-day course of either oral amoxicillin/clavulanate, oral sultamicillin (a pro-drug of ampicillin/sulbactam), or oral clindamycin (for suspected or confirmed penicillin allergy). The primary outcome was a composite of any infection related to emergency caesarean section, surgical site infections (SSI), endometritis, and persistent fever of unknown aetiology within 30 days of surgery. The secondary outcomes were individual components of the primary outcome. We used multivariable logistic regression with landmark analysis to estimate the adjusted odds ratio (aOR) and 95% confidence interval (95% CI). Among 2653 included records (mean age 28.9, 15.2% being obese, 32.9% having no comorbidities), ruptured membranes (40.6%) and foetal distress (23.3%) were the 2 most common indications of emergency caesarean section. There were no significant differences in the risk of developing the primary outcome (aOR 0.86, 95% CI 0.70 to 1.05, p = 0.148) or the secondary outcomes (any infection related to emergency caesarean section [aOR 0.84, 95% CI 0.68 to 1.04], SSI [aOR 0.80, 95% CI 0.60 to 1.06], endometritis [aOR 0.92, 95% CI 0.61 to 1.39], and persistent fever of unknown aetiology [aOR 0.93, 95% CI 0.67 to 1.28]). We found limited evidence for a lower risk of the primary outcome in women receiving ScAP with age ≥ 35 years (aOR 0.76, 95% CI 0.58 to 0.99) or with obesity (aOR 0.58, 95% CI 0.35 to 0.97). Among women with low-to-moderate risk of postpartum infection, there was no significant difference in the risk of developing maternal infection after emergency caesarean section between SPoC and SPoC + ScAP groups. Women of older age (≥ 35 years) or with obesity may benefit from ScAP, but further confirmatory research is needed. Not applicable.