Abstract Background No dietary factors have yet been shown to conclusively impact the incidence of microscopic colitis (MC). Here, we sought to examine the relationship between alcohol intake and the risk of MC. Methods We conducted a prospective cohort study of 209,902 participants (age range, 28.5–66.7 years) enrolled in the Nurses’ Health Study (NHS) and Nurses’ Health Study II (NHSII). Validated data on alcohol consumption were collected at baseline in 1986 in the NHS and 1991 in the NHSII and updated every 4 years. Diagnoses of MC were confirmed via review of histopathology data. We used Cox proportional hazards modeling to estimate adjusted hazard ratios (aHRs) and 95% confidence intervals (CIs). Results Through 2016 in the NHS and 2017 in the NHSII, we confirmed 352 incident cases of MC over 4,994,324 person-years. Higher alcohol consumption was associated with an increased risk of MC (Ptrend < .001). Compared to non-users, the aHRs of MC were 1.20 (95% CI, 0.86–1.67) for consumers of 0.1–4.9 g/day of alcohol, 1.90 (95% CI, 1.34–2.71) for consumers of 5–14.9 g/day, and 2.31 (95% CI, 1.54–3.46) for consumers of ≥15 g/day. The associations were consistent across the histologic subtypes of collagenous and lymphocytic colitis (Pheterogeneity = .523). When stratified by alcohol type, the risk according to every 2 servings/week appeared to be strongest with consumption of wine (aHR, 1.08; 95% CI, 1.04–1.12) as compared to beer (aHR, 1.01; 95% CI, 0.91–1.12) or liquor (aHR, 1.00; 95% CI, 0.92–1.09). Conclusions Alcohol consumption was associated with an increased risk of MC. Further studies are needed to determine the mechanism underlying these associations, as well as the impact of reducing alcohol intake in patients with MC.