<p>This study aims to examine how HIV prevention tools were used and how they clustered together among men who have sex with men (MSM) testing at a community-based sexual health center in Lisbon, Portugal, from 2014 to 2021. We used data from 16,780 visits from adult cisgender MSM and had an HIV-negative test result at baseline in the Lisbon Cohort of MSM—an open, prospective cohort study conducted at CheckpointLX, a community-based sexual health center tailored to MSM, from 2014 to 2021. A longitudinal clustering approach was used to identify clusters of HIV prevention (<i>cluster</i> package for R). Six clusters of HIV prevention were identified: condom use (9,109 visits); low or no condom use, low PrEP (preexposure prophylaxis) use (6,258 visits); anal sex abstinence (746 visits); PEP (postexposure prophylaxis) and condom use (305 visits); PEP use (186 visits); and PrEP and condom use (176 visits). Most participants were aged 24 to 34 years old, were born in Portugal, had high education, and self-identified as gay. PrEP and PEP uptake were more associated with being born in Brazil, while low prevention adherence was less associated with high education. Condom use was the most frequently reported prevention strategy, followed by the low or no condom use, low PrEP use cluster. However, participants with higher odds of reporting HIV risk behaviors were the ones allocated to clusters with reports of higher frequency of prevention tools utilization.</p>