Moderate alcohol consumption is widespread but its impact on brain structure and function is contentious. The relationship between alcohol intake and structural and functional neuroimaging indices, the threshold intake for associations, and whether population subgroups are at higher risk of alcohol-related brain harm remain unclear. 25,378 UK Biobank participants (mean age 54.9 ± 7.4 years, 12,254 female) underwent multi-modal MRI 9.6 ± 1.1 years after study baseline. Alcohol use was self-reported at baseline (2006–10). T1-weighted, diffusion weighted and resting state images were examined. Lower total grey matter volumes were observed in those drinking as little as 7–14 units (56–112 g) weekly. Higher alcohol consumption was associated with multiple markers of white matter microstructure, including lower fractional anisotropy, higher mean and radial diffusivity in a spatially distributed pattern across the brain. Associations between functional connectivity and alcohol intake were observed in the default mode, central executive, attention, salience and visual resting state networks. Relationships between total grey matter and alcohol were stronger than other modifiable factors, including blood pressure and smoking, and robust to unobserved confounding. Frequent binging, higher blood pressure and BMI steepened the negative association between alcohol and total grey matter volume. In this large observational cohort study, alcohol consumption was associated with multiple structural and functional MRI markers in mid- to late-life.