Gay, bisexual and other men who have sex with men are disproportionately affected by HIV in Guatemala; interpersonal violence may increase behaviours that augment the risk of HIV in this group. Although 44% of Guatemalans identify as Indigenous, little information exists on the experiences of Indigenous sexual minority individuals. In this study, we sought to compare different forms of violence and HIV-related behaviours by Indigenous identity among gay, bisexual and other men who have sex with men; and determine if associations between violence and HIV-related behaviours differed by Indigenous identity. We used cross-sectional survey data from 716 Spanish-speaking, adult men recruited from urban centres to examine the prevalence of and relationship between different forms of interpersonal violence and HIV-related behaviours using logistic regression analyses, including the moderating effect of Indigenous identity. In general, fewer Indigenous participants reported interpersonal violence victimisation and HIV-related behaviours compared to their non-Indigenous counterparts. In weighted multivariable analyses, non-Indigenous participants who reported physical and/or sexual violence were over five times as likely to report transactional sex (OR = 5.17, 95% CI 2.11-12.68, p  < 0.001), but the relationship was not significant for Indigenous participants. Findings suggest that Indigenous sexual minority men have unique contexts and that additional strengths-based research is needed to ensure that actions and efforts to promote violence and HIV prevention meet their needs.