Abstract Introduction Victimization based on sexual orientation or gender identity is a cause for concern. Bias-motivated violence affect not only the individuals targeted but also their communities and societies as a whole. Objective To estimate the proportion of bias-motivated victimization among cisgender men who have sex with men (MSM) and to compare sociodemographic and behavioral characteristics and HIV and syphilis test results between victims and non-victims. Methods We used data from the baseline visit of 2811 adult cisgender MSM from July 2017 to December 2020 in the Lisbon Cohort of MSM. Victimization was defined as self-reported lifetime or recent (in the previous 12 months) experience of physical or verbal violence motivated by sexual orientation or gender identity. Rapid HIV and syphilis tests determined serostatus. We conducted descriptive statistics to summarize the sociodemographic and behavioral characteristics and the prevalence of victimization and compared groups using the Student t-test or Mann–Whitney U test and chi-square test, as appropriate. Results Overall, 40.3% of participants reported lifetime bias-motivated physical or verbal violence, and 11.7% reported recent victimization. Recent victimization contexts more frequently reported were street/neighborhood (67.9%) and workplace/school (35.5%). Victimization was associated with younger age (mean age: 26.5 vs 30.2, p-value < 0.001), being born in Brazil or other American countries, or being 14 or younger at their anal intercourse with a man debut (19.5% vs. 11.0%, p-value < 0.001). Lifetime victimization was not significantly associated with reactive results for HIV (p-value = 0.135) or syphilis (p-value = 0.760). Conclusion The violence motivated by sexual orientation or gender identity was quite frequent in this community. The occurrence of violence based on sexual orientation or gender identity in the Lisbon Cohort of MSM was associated with adverse social conditions and health risk behaviors. Policy Implications Raising awareness about bias-motivated violence as a hate crime may deter potential aggressions. Primary violence prevention should tackle specificities of sexual and gender minorities.