BACKGROUND: Noncommunicable diseases (NCDs), specifically diabetes and hypertension, are rising in high HIV-burdened countries such as South Africa. How integrated HIV care into primary health care (PHC) influences NCD care is unknown. We aimed to understand whether differences existed in NCD care (pre- versus post-integration) and how changes may relate to HIV patient numbers. SETTING: Public sector PHC clinics in Free State, South Africa. METHODS: Using a quasiexperimental design, we analyzed monthly administrative data on 4 indicators for diabetes and hypertension (clinic and population levels) during 4 years as HIV integration was implemented in PHC. Data represented 131 PHC clinics with a catchment population of 1.5 million. We used interrupted time series analysis at ±18 and ±30 months from HIV integration in each clinic to identify changes in trends postintegration compared with those in preintegration. We used linear mixed-effect models to study relationships between HIV and NCD indicators. RESULTS: Patients receiving antiretroviral therapy in the 131 PHC clinics studied increased from 1614 (April 2009) to 57, 958 (April 2013). Trends in new diabetes patients on treatment remained unchanged. However, population-level new hypertensives on treatment decreased at ±30 months from integration by 6/100, 000 (SE = 3, P < 0.02) and was associated with the number of new patients with HIV on treatment at the clinics. CONCLUSIONS: Our findings suggest that during the implementation of integrated HIV care into PHC clinics, care for hypertensive patients could be compromised. Further research is needed to understand determinants of NCD care in South Africa and other high HIV-burdened settings to ensure patient-centered PHC.