Abstract Introduction To prioritize and tailor interventions for ending AIDS by 2030 in Africa, it is important to characterize the population groups in which human immunodeficiency virus (HIV) viraemia is concentrating. Methods We analysed HIV testing and viral load data collected between 2013 and 2019 from the open, population-based Rakai Community Cohort Study in Uganda, to estimate HIV seroprevalence and population viral suppression over time by gender, 1-year age bands, and residence in inland and fishing communities. All estimates were standardized to the underlying source population by using census data. We then assessed 95–95–95 targets in their ability to identify the populations in which viraemia is concentrated. Results Following the implementation of Universal Test and Treat, the proportion of individuals with viraemia decreased from 4.9% (4.6%–5.3%) in 2013 to 1.9% (1.7%–2.2%) in 2019 in inland communities and from 19.1% (18.0%–20.4%) in 2013 to 4.7% (4.0%–5.5%) in 2019 in fishing communities. Viraemia did not concentrate in the age and gender groups furthest from achieving 95–95–95 targets. Instead, in both inland and fishing communities, women aged 25–29 years and men aged 30–34 years were the 5-year age groups that contributed most to population-level viraemia in 2019, despite these groups being close to or having already achieved 95–95–95 targets. Conclusion The 95–95–95 targets provide a useful benchmark for monitoring progress towards HIV epidemic control, but do not contextualize underlying population structures and so may direct interventions towards groups that represent a marginal fraction of the population with viraemia.