Background The East Central (EC) region of Uganda has the least viral suppression rate despite having a relatively low prevalence of human immunodeficiency virus (HIV). Although the viral suppression rate in Kamuli district is higher than that observed in some of the districts in the region, the district has one of the largest populations of people living with HIV (PLHIV). We sought to examine the factors associated with viral suppression after the provision of intensive adherence counselling (IAC) among PLHIV in the district. Methods We reviewed records of PLHIV and used them to construct a retrospective cohort of patients that started and completed IAC during January – December 2019 at three high volume HIV treatment facilities in Kamuli district. We also conducted key informant interviews of focal persons at the study sites. We summarized the data descriptively, tested differences in the outcome (viral suppression after IAC) using chi-square and t-tests, and established independently associated factors using log-binomial regression analysis with robust standard errors at 5% statistical significance level using STATA version 15. Results We reviewed 283 records of PLHIV. The mean age of the participants was 35.06 (SD 18.36) years. The majority of the participants were female (56.89%, 161/283). The viral suppression rate after IAC was 74.20% (210/283). The most frequent barriers to ART adherence reported were forgetfulness 166 (58.66%) and changes in the daily routine 130 (45.94). At multivariable analysis, participants that had a pre-IAC viral load that was greater than 2000 copies/ml [adjusted Prevalence Risk Ratio (aPRR)= 0.81 (0.70 - 0.93), p=0.002] and those that had a previous history of viral load un-suppression [aPRR= 0.79 (0.66 - 0.94), p=0.007] were less likely to achieve a suppressed viral load after IAC. ART drug shortages were rare, ART clinic working hours were convenient for clients and ART clinic staff received training in IAC. Conclusion Despite the consistency in drug availability, counselling training, flexible and frequent ART clinic days, the viral suppression rate after IAC did not meet recommended targets. A high viral load before IAC and a viral rebound were independently associated with having an unsuppressed viral load after IAC. IAC alone may not be enough to achieve viral suppression among PLHIV. To improve viral suppression rates after IAC, other complementary services should be paired with IAC.