Individuals are initiating antiretroviral therapy (ART) at earlier HIV disease stages. Unhealthy alcohol use is a known barrier to successful HIV treatment outcomes, yet it is unclear whether the problem varies by disease stage. We measured alcohol use with an objective biomarker (phosphatidylethanol [PEth]), comparing individuals (n = 401) with early (CD4 > 350 cells/mL, WHO Stage 1) versus late (CD4 < 200 cells/mL) ART initiation in HIV care in Uganda and South Africa (SA). We examined the association between CD4 count and biomarker results using multivariable regression modeling, and compared PEth results to self-report to assess underreporting. Overall, 32.2% (n = 129) had unhealthy alcohol use (PEth ≥ 50 ng/ml). Early ART initiation was significantly associated with unhealthy alcohol use in Uganda (AOR 2.65; 95% CI: 1.05–6.72), but not SA (AOR 1.00; 95% CI: 0.46–2.17). In Uganda, 23.2% underreported unhealthy alcohol use versus 11.6% in SA (χ2 = 9.30; p < 0.01). Addressing unhealthy alcohol use is important as patients initiate ART earlier, yet challenging due to underreporting.