The study aimed to determine the prevalence and associated factors of microalbuminuria among patients infected with human immunodeficiency virus (HIV). A cross-sectional study was conducted at the Infectious Disease Control Center of Princess Marina Hospital, a Tertiary Clinic in Gaborone, Botswana. The risk factors of microalbuminuria were determined by comparing the sociodemographic and clinical characteristics of patients with the presence of microalbuminuria or normoalbuminuria. In total, 297 randomly selected HIV-infected patients were included in the analysis. The mean age of the study participants was 48.6 years, with the majority of patients (60.9%) being females. The study participants were largely well-controlled both immunologically and virologically, with 283/297 (95.3%) and 280/297 (94.3%), having CD4 counts of more than 200 cells/mm3 and undetected viral load (<400 copies/mL), respectively. The prevalence of microalbuminuria was found to be 46.5%. Microalbuminuria was associated with the duration of exposure to a regimen containing tenofovir [P <0.001, odds ratio = 1.137, 95% confidence interval (CI) = 1.073–1.205] and a history of diabetes mellitus (P = 0.044, odds ratio = 9.260, 95% CI = 1.058–81.06). Sociodemographic characteristics and other clinical factors were not associated with microalbuminuria. There is a need to carry out prospective studies among HIV- infected patients with microalbuminuria to determine the short- and long-term cardiovascular morbidity and mortality outcomes.