Background <p>The COVID-19 pandemic significantly disrupted healthcare systems. In France, non-urgent procedures were postponed, leading to a 52% decrease in elective surgical activity in public hospitals in Paris during the first wave. We aimed to assess the impact on gastro-intestinal emergency surgeries of health strategies implemented during this pandemic.</p> Methods <p>This multicenter retrospective cohort study enrolled patients from sixteen public hospitals over five periods: March and April, 2018, and 2019 (pre-pandemic), 2020 (first wave), 2021 (third wave), and 2022 (post-pandemic). All adult patients requiring urgent gastrointestinal surgery admitted through the Emergency Department were included. Statistical tests were performed with the chi-square test, ANOVA test, Student test, Kruskall Wallis or Fisher exact test. Univariate and multivariate logistic regression were performed to investigate the relationship between mortality at day 90 and the primary data recorded.</p> Results <p>2692 patients’ stay were included: 54% male, median age 48 [32;68], 12% ICU admission rate, median Charlson score 2 [0;5], and 6% mortality rate at day 90. The number of abdominal emergency cases decreased during the first wave (− 37% in 2020 compared to 2019). In the multivariate regression model, ICU admission, Charlson comorbidity score, and surgery in 2020 were independently associated with mortality at day 90 (as hospital length of stay, to a lower extent).</p> Conclusion <p>Undergoing emergency surgery during the first lockdown was an independent mortality risk factor, independent of the COVID-19 infectious status. Whatever major healthcare issue is ongoing, all efforts should be made to maintain healthcare access to all, including urgent surgical procedures.</p> <p><i>Trial registration</i>: Not applicable.</p>