Background We explored the association between alcohol use and condomless receptive (CRAI) and insertive (CIAI) anal intercourse within partnership contexts of men who have sex with men (MSM) and transgender women (TGW) in Lima, Peru. Methods From 2012–2014, we surveyed men and TGW (n = 1607) who reported anal intercourse with ≥1 male or TGW. Alcohol use with up to 3 sexual partners during the prior 90 days was evaluated. Bivariate and multivariate analyses used generalized estimating equations to assess event-level associations between alcohol use, CRAI, CIAI, and partnership characteristics while adjusting for participant clustering from multiple partners. Results Of 4774 sexual partnerships reported, 48% were casual, 34% primary, 10% anonymous, and 8% commercial. Alcohol use preceding sex was significantly (p < 0.05) associated with CRAI (PR = 1.26) and CIAI (PR = 1.37). Partnership characteristics significantly associated with alcohol use included commercial sex work (PR = 2.21) and trended (p < 0.10) towards alcohol use with casual (PR = 1.16), transgender (PR = 1.48), and moderno (“versatile”; PR = 1.17) partners. CRAI and CIAI were more common among participants who reported knowing they (PR = 1.52; PR = 1.41, respectively) or their partner (PR = 1.47; PR = 1.44, respectively) was HIV-uninfected. Yet, only CIAI (PR = 1.42) was more commonly reported with known HIV-infected partners. Participants who drank alcohol prior to sex were less likely to know their partner's HIV serostatus. Conclusions Alcohol use prior to intercourse was associated with CRAI and CIAI, varied by partnership type, and may impair knowledge of partner HIV serostatus. Detailed knowledge of alcohol use within partner-specific contexts is essential for informing condom-based and alternative HIV prevention strategies for MSM and TGW in Peru.