Strengthening strategies to improve adherence to the use of pre-exposure prophylaxis (PrEP) in key populations constitutes a global health priority to be achieved across countries, especially in countries that share a high flow of people such as Brazil and Portugal. This study aimed to analyze the factors associated with adherence to PrEP among MSM from two Portuguese-speaking countries, highlighting the opportunities and preventive strategies for the global health scenario. This was a cross-sectional analytical online survey conducted from January 2020 to May 2021 with MSM in Brazil and Portugal. For analysis of the data, the Poisson regression model was used to estimate the prevalence ratio (PR) for developing a model to evaluate the associated factors in both countries in a comparative and isolated way. Adherence to PrEP use corresponded to 19.5% (n = 1682) of the overall sample: 18.3% (n = 970) for Brazil and 21.5% (n = 712) for Portugal. Having more than two sex partners in the last 30 days (aPR: 30.87) and routinely undergoing HIV tests (aPR: 26.21) increased the use of this medication. Being an immigrant (PR: 1.36) and knowing the partner’s serological status (PR: 1.28) increased adherence to PrEP in Portugal, whereas, in Brazil, it was being an immigrant (PR: 0.83) and not knowing the serological status (PR: 2.24) that promoted the use of this medication. Our findings reinforce the need to invest in programs and strategies to improve access and adherence to PrEP, especially in key populations.