Background Severe COVID-19 is associated with immune dysregulation, microbiome disruption, and increased vulnerability to secondary infections. However, the longer-term risk of acute gastroenteritis (AGE) following COVID-19 remains poorly studied. We compared AGE incidence among community-managed and hospitalised COVID-19 patients with test-negative controls and hospitalised sepsis patients. Methods We conducted a retrospective cohort study using electronic healthcare data. Patients with a recorded SARS-CoV-2 PCR test between 01 March 2020 and 01 March 2022 were allocated to test-negative, community COVID-19, or hospitalised COVID-19 cohorts. A hospitalised sepsis cohort was assembled for an age-, sex- and time-matched analysis. AGE incidence rates were calculated for the two years before enrolment and during follow-up. Negative binomial regression and conditional Poisson models estimated incidence rate ratios (IRRs) adjusting for demographic and clinical covariates. Results Among 788 103 patients, AGE incidence in the pre-pandemic period was higher among individuals later hospitalised with COVID-19 or sepsis compared with community cases. During follow-up, AGE incidence was slightly lower in community COVID-19 cases than test-negative controls (adjusted IRR 0.88 [95% CI 0.85-0.92]), but substantially higher among hospitalised COVID-19 patients (IRR 5.80 [95% CI: 5.38-6.25]). Matched analyses confirmed increased AGE rates compared with community controls (IRR 4.63 [95% CI: 4.15-5.17]) and hospitalised sepsis controls (IRR 1.41 [95% CI 1.21-1.64]). Conclusions COVID-19 hospitalisation is associated with a marked increase in AGE risk after discharge, exceeding that associated with sepsis hospitalisation. By contrast, lower AGE rates in community COVID-19 cases likely reflect baseline differences rather than protective effects of infection. Overall, these findings demonstrate heightened post discharge vulnerability to gastrointestinal illness after COVID 19 hospitalisation and support the need for improved follow up and surveillance strategies.