Coronavirus disease 2019 caused significant negative damage to the health status of populations and health systems globally. In Uganda, our previous study revealed that the strict Public Health and Social measures (PHSMs) and the closure of Entebbe Regional Referral Hospital (ERRH) led to missed healthcare access among the citizens in the Entebbe municipality. Limited studies, however, exist on the impact of the response measures on the local health systems. This study aims to explore the impacts of these measures on the local health service provision from the views of health facilities in Entebbe. We used a thematic framework method, grounded by the health systems resilience framework consisting of five components: (1) health service delivery; (2) medical products and technology; (3) health workforce; (4) public health functions; and (5) governance and financing. Key informant interviews with eight representatives from four private hospitals and four health centers were conducted from September to October 2022. Fifteen themes and 25 subthemes were identified. With the closure of the ERRH and the strict PHSMs, the citizens faced various difficulties in accessing the needed health services. The facilities received an overwhelming number of patients and faced various challenges, such as a lack of medicine, healthcare workers, facility capacity, and no means to transfer patients. Nevertheless, the facilities made efforts to maintain the required services. Moreover, mobilizing vertical and horizontal actors through a flexible network, from the district health office to community health volunteers, helped to coordinate the medicines, transportation for both patients and healthcare workers, conduct patient tracking, etc. Our study suggested the importance of an integrated system of public health and health service delivery systems, the formalization of a vertical cooperative mechanism, and the introduction of public health insurance for strengthening resilient health systems. These insights may benefit other sub-Saharan cities.