HIV prevention programs typically focus on changing individuals' risk behaviors, often without considering the socioecological factors that can moderate this risk. We characterized HIV risk among men who have sex with men (MSM) in Indonesia (n = 1314) using latent class analysis and used multinomial logistic regression to identify latent class relationships with demographics, social/sexual networks, and community-level socioecological indicators of HIV risk. Three HIV risk latent classes were identified-"Sexually Moderate" (n = 333), "Sexual Explorative" (n = 575), and "Navigating Complexities" (n = 406). Using "Sexually Moderate" (lowest risk) as the reference group, MSM in the "Sexual Explorative" class had additional social/sexual network-level risks (meeting partner(s) using both online and offline methods [RR = 3.8; 95%CI 1.7-8.6] or general social media and gay-specific online platforms [RR = 2.6; 95%CI 1.9-3.6] to meet partners, group sex [RR = 10.9; 95%CI 4.5-25.4], transactional sex [RR = 1.6; 95%CI 1.2-2.2]), and community-level risks (experiencing homosexual-related assaults [RR = 1.4; 95%CI 1.1-1.9]). MSM in the "Navigating Complexities" class had additional social/sexual network-level risks (low social support [RR = 1.6; 95%CI 1.1-2.5], less disclosure of their sexuality [RR = 1.4; 95%CI 1.0-1.9]) and community-level risks (higher internalized homonegativity scores [RR = 1.2; 95%CI 1.1-1.4], ever experiencing homosexual-related assaults [RR = 1.4:95%CI 1.1-1.9], less exposure to HIV/STI health promotion [RR = 0.7; 95%CI 0.5-0.9], attending STI-related services in the past 6 months [RR = 0.6; 95%CI 0.4-0.8]). Co-occurring individual and socioecological risk recommend holistic HIV prevention strategies tailored to consider the social and structural conditions of MSM in Indonesia are needed.