As international guidelines increase access to antiretroviral therapy (ART) globally, ART adherence becomes increasingly important to achieve HIV treatment as prevention (TasP) goals. In the concentrated HIV epidemic among men who have sex with men (MSM) and transgendered women (TGW) in Lima, Peru, the independent correlates of ART nonadherence were examined to inform treatment intervention priorities. Cross sectional survey of HIV-infected MSM and TGW who are engaged in clinical care in Lima, Peru. From June to August 2012, 302 HIV-infected Peruvian MSM/TGW from three clinical care sites were recruited using convenience sampling to participate in a cross-sectional computer-assisted adherence survey. Several standardized screening measures associated with ART nonadherence were examined in order to determine the independent correlates of optimal (≥90%) and perfect (100%) adherence, which were assessed using logistic regression. Of the 302 participants recruited, 263 (87.1%) were prescribed ART. Among those prescribed ART, 229 (87.1%) reported optimal and 146 (55.5%) reported perfect adherence. The prevalence of alcohol use disorders (AUD; 43.2%), alcohol dependence (5.3%), recent drug use (6.0%), and depression (44.5%) was high, and most participants had some evidence of neurocognitive impairment. Meeting criteria for having an AUD and depression were collinear (p < 0.001). On multivariate analysis, having an AUD was inversely related and the only independent correlate of optimal (AOR = 0.427; 95% CI = 0.187-0.976) and perfect (AOR = 0.552; 95% CI = 0.327-0.930) ART adherence. AUDs are highly prevalent among Peruvian HIV-infected MSM and contribute significantly to ART nonadherence. These findings support the need for screening and treating underlying AUDs. In order to meet HIV TasP goals, evidence-based strategies targeting AUDs are likely to directly improve ART adherence and indirectly improve overall individual health, HIV treatment engagement, and reduce transmission to sexual partners among this vulnerable and disproportionally affected population.