Background: Pre-exposure prophylaxis (PrEP) scale-up is urgent to reduce new HIV cases among gay, bisexual, and other men who have sex with men (MSM) in Latin America. Different PrEP modalities may increase PrEP uptake and adherence, especially among young MSM. Objectives: To assess preferences for PrEP modalities among MSM from Brazil, Mexico, and Peru. Design: Cross-sectional web-based study (March-May 2018) targeting MSM through advertisements on Grindr, Hornet, and Facebook. We included MSM aged ⩾ 18 years and who reported HIV-negative status. Methods: We assessed preferences for PrEP modalities with the following question: 'Considering that all following PrEP modalities were available, which one would you prefer considering a scale from 1 to 3 (1 = most preferred): daily oral PrEP, event-driven PrEP (ED-PrEP), and long-acting injectable PrEP'. We assessed factors associated with each most preferred PrEP modality per country using multivariable logistic regression models. Results: A total of 19,457 MSM completed the questionnaire (Brazil: 58%; Mexico: 31%; Peru: 11%); median age was 28 years [interquartile range (IQR): 24-34]. Overall, injectable PrEP was the most preferred modality [42%; 95% confidence interval (CI): 41-43], followed by daily PrEP (35%; 95% CI: 34-35), and ED-PrEP (23%; 95% CI: 23-24). In multivariable models, preferring injectable PrEP was associated with PrEP awareness in all three countries, while PrEP eligibility only in Brazil. Preferring daily PrEP was associated with younger age and lower income in Brazil and Mexico, and lower education only in Brazil. The odds of preferring ED-PrEP were lower among MSM aware and eligible for PrEP in Brazil and Mexico. Conclusions: Long-acting injectable PrEP was the preferred PrEP modality among MSM in Brazil, Mexico, and Peru, especially those aware and eligible for PrEP. Public health interventions to increase PrEP modalities literacy and availability in Latin America are urgent especially among MSM of young age, lower income, and lower education.