Background Acute Kidney Injury (AKI) is a frequent and serious postoperative complication in trauma or critically ill patients in the intensive care unit. We aimed to estimate the risk of AKI following major emergency abdominal surgery and the association between AKI and 90-day postoperative mortality. Methods In this retrospective cohort study, we included patients undergoing major emergency abdominal surgery at the Department of Surgery, Zealand University Hospital, Denmark, from 2010 to 2016. The primary outcome was the occurrence of AKI within postoperative day seven (POD7). AKI was defined according to the Kidney Disease: Improving Global Outcomes (KDIGO)-criteria. The risk of AKI was analysed with a multivariable logistic regression. The association between AKI and 90-day mortality was analysed with a multivariable survival analysis. Results In the cohort, 122 out of 703 (17.4%) surgical patients had AKI within POD7. Of these, 82 (67.2%) had AKI stage 1, 26 (21.3%) had AKI stage 2, and 14 (11.5%) had AKI stage 3. Fifty-eight percent of the patients who developed postoperative AKI did so within the first 24 h of surgery. Ninety-day mortality was significantly higher in patients with AKI compared with patients without AKI (41/122 (33.6%) versus 40/581 (6.9%), adjusted hazard ratio 4.45 (95% confidence interval 2.69–7.39, P < 0.0001)), and rose with increasing KDIGO stage. Pre-existing hypertension and intraoperative peritoneal contamination were independently associated with the risk of AKI. Conclusions The risk of AKI is high after major emergency abdominal surgery and is independently associated with the risk of death within 90 days of surgery.