In Lima, Peru, men who have sex with men (MSM) and transgender women (TW) are disproportionately affected by HIV. Patterns of sexual behavior vary by sexual partner type, which has implications for HIV prevention intervention design. We examine correlates of sex and condomless anal intercourse (CAI) with each of four types of partners among HIV-negative MSM and TW in Lima who completed monthly questionnaires about partnership types and CAI. Odds ratios were calculated using generalized estimating equations to identify correlates of being in different types of partnerships and CAI within those partnerships. Among 1,831 MSM and TW with over 14,792 study visits, CAI was most reported with main partners, followed by casual partners, one-time partners, and clients. Presence of an alcohol use disorder (AUD) significantly increased the odds of CAI with all types of partners (main: OR 1.36 (95% CI 1.17-1.57); casual: 1.49 (1.27-1.75); one-time: 1.45 (1.22-1.72); client 1.52 (1.12-2.08)); recent alcohol use increased odds of CAI with main partners. Having one main partner decreased the odds of being in casual and one-time partnerships and of CAI in all types of partnerships. Interventions targeting AUDs and individuals with multiple sexual contacts could reduce CAI and HIV risk in this population. Clinical trial registration: The Sabes study was registered in March 2013 with the National Institutes of Health at ClinicalTrials.gov (identifier: NCT01815580).