Background During the COVID-19 pandemic, an increase of heavy alcohol use has been reported in several high-income countries. We examined changes in alcohol use during the pandemic among primary health care (PHC) patients in two middle income countries, Colombia and Mexico. Methods Data were collected during routine consultations in 34 PHC centres as part of a large-scale implementation study. Providers measured patients' alcohol consumption with the three item 'Alcohol Use Disorders Identification Test' (AUDIT-C). Generalized linear mixed models were performed to examine changes in two dependent variables over time (pre-pandemic and during pandemic): 1) the AUDIT-C score and 2) the proportion of heavy drinking patients (8+ on AUDIT-C). Results Over a period of more than 600 days, data from N = 17 273 patients were collected. During the pandemic, the number of patients with their alcohol consumption measured decreased in Colombia and Mexico. Each month into the pandemic was associated with a 1.5% and 1.9% reduction in the mean AUDIT-C score in Colombia and Mexico, respectively. The proportion of heavy drinking patients declined during the pandemic in Colombia (pre-pandemic: 5.4%, 95% confidence interval (CI) = 4.8% to 6.0%; during the pandemic: 0.8%, 95% CI = 0.6% to 1.1%) but did not change in Mexico. Conclusions Average consumption levels declined and the prevalence of heavy drinking patterns did not increase. In addition to reduced opportunities for social drinking during the pandemic, changes in the population seeking PHC and restrictions in alcohol availability and affordability are likely drivers for lower levels of alcohol use by patients in this study.