Background: The Zambia National Health Strategic Plan (ZNHSP) 2011–2017 underscores the need for community-level risk factor stratification to bolster insufficient incidence and prevalence data. This study evaluates the prevalence and incidence of hypertension and diabetes mellitus in HIV-infected patients on Highly Active Anti-Retroviral Therapy (HAART) and assesses associations with ARV use. Methodology: A retrospective cohort analysis was conducted using the SMART CARE database in Chongwe district, involving 2070 HIV-infected persons on HAART. Statistical analysis included Chi-square, Kruskal-Wallis tests, and logistic regression. Results: Among participants, 33.8% exhibited hypertension, with an incidence case fatality rate of 85.7 per 1000 person-years (PYFU). Hypertension was notably higher in men (64%) than women (49%) and prevalent in the 18–45 age group (57.2%). The incidence of type II diabetes was 37.4 per 1000 PYFU. Logistic regression highlighted significant predictors for both conditions, including ART combination, age, and smoking status. Conclusion: High prevalence and incidence rates of hypertension and type II diabetes were observed among HIV-positive individuals on HAART. Certain HAART combinations, particularly twoNRTIs plus a PI or INSTI, correlated with increased hypertension risk, while combinations including NNRTI or INSTI were linked to higher diabetes incidence.