Primary health care clinics in South Africa were confronting substantial population burdens of HIV and non-communicable disease (NCD) with limited resources even prior to the Covid-19 pandemic. Care outcomes and implementation of new programs vary between clinics in the same settings; qualitative research suggests that clinic factors such as leadership may play a key role in optimizing primary care. We propose a secondary analysis to test whether clinic climate in rural South Africa helps to explain health outcomes for individual on treatment for HIV and/or for hypertension before and during the Covid-19 pandemic. Working with collaborators at the Agincourt Health and Demographic Surveillance System (HDSS) in Mpumalanga Province, we will combine detailed data from a 2019 quality assessment of 9 clinics with longitudinal patient data for over 25,000 individuals from 2019 to 2021. Exposures of interest include measures of leadership, stress, and cohesion within clinics. The primary outcome for both HIV and hypertension is patient retention in treatment; secondary outcomes include disease control, appropriate referral to decentralized care, and hospitalization. We will use generalized estimating equation models to test whether clinic measures are associated with better patient outcomes prior to the Covid-19 pandemic (March 2019 - Feb 2020) as well as during the pandemic (March 2020 - Feb 2021) for each condition. We aim to understand which elements of clinic climate shape patient outcomes and what aspects of population health are most strongly impacted during routine and crisis situations. With key stakeholders in the HDSS, we will use the findings to design an intervention to strengthen clinics and improve HIV and NCD services. The findings have implications for rural health services in resource-constrained settings as policy makers confront the need for stronger, more integrated primary health care services in the wake of Covid-19.