Background Diabetes and hypertension are increasingly important population health challenges in Eswatini. Prior to this project, healthcare for these conditions was primarily provided through physician-led teams at tertiary care facilities and accessed by only a small fraction of people living with diabetes or hypertension. This trial tests and evaluates two community-based healthcare service models implemented at the national level, which involve health care personnel at primary care facilities and utilize the country’s public sector community health worker cadre (the rural health motivators [RHMs]) to help generate demand for care. Methods This study is a cluster-randomized controlled trial with two treatment arms and one control arm. The unit of randomization is a primary healthcare facility along with all RHMs (and their corresponding service areas) assigned to the facility. A total of 84 primary healthcare facilities were randomized in a 1:1:1 ratio to the three study arms. The first treatment arm implements differentiated service delivery (DSD) models at the clinic and community levels with the objective of improving treatment uptake and adherence among clients with diabetes or hypertension. In the second treatment arm, community distribution points (CDPs), which previously targeted clients living with human immunodeficiency virus, extend their services to clients with diabetes or hypertension by allowing them to pick up medications and obtain routine nurse-led follow-up visits in their community rather than at the healthcare facility. In both treatment arms, RHMs visit households regularly, screen clients at risk, provide personalized counseling, and refer clients to either primary care clinics or the nearest CDP. In the control arm, primary care clinics provide diabetes and hypertension care services but without the involvement of RHMs and the implementation of DSD models or CDPs. The primary endpoints are mean glycated hemoglobin (HbA1c) and systolic blood pressure among adults aged 40 years and older living with diabetes or hypertension, respectively. These endpoints will be assessed through a household survey in the RHM service areas. In addition to the health impact evaluation, we will conduct studies on cost-effectiveness, syndemics, and the intervention’s implementation processes. Discussion This study has the ambition to assist the Eswatini government in selecting the most effective delivery model for diabetes and hypertension care. The evidence generated with this national-level cluster-randomized controlled trial may also prove useful to policy makers in the wider Sub-Saharan African region. Trial registration NCT04183413. Trial registration date: December 3, 2019