Background In response to the growing burden of chronic diseases in sub-Saharan Africa, where innovative and cost-effective health solutions are imperative, this study outlines a protocol for a cluster-randomized trial that compares integrated community-based care with integrated facility-based care to improve access and outcomes for patients with HIV, diabetes, or hypertension. Methods & analysis We will conduct a pragmatic cluster-randomized trial comparing integrated community care with integrated facility care in Tanzania and Uganda. Patients living with HIV, diabetes, or hypertension, stable on treatment in health facilities, will be organised into groups of approximately 8–14 persons and randomly assigned to integrated community or facility-based care. The study has two co-primary endpoints: a composite endpoint of glycemia and blood pressure control among individuals with diabetes and/or hypertension and suppression of plasma viral load among people living with HIV. Participants will receive their drugs, adherence support, and monitoring at a community venue in the integrated community arm. Those randomised to the control arm will receive integrated facility-based care. All study participants will be followed up for 12 months. A sample size of 116 groups will provide over 80% power to detect an absolute difference in blood pressure and blood glucose control of 10% at the 5% two-sided significance level. For HIV viral suppression, the trial will have over 80% power to show non-inferiority with a delta margin = 8.5%, 7.5%, and 5.5% assuming viral suppression is 85%, 90% and 95% respectively. To allow for loss to follow-up, our target for enrolment is 124 groups, each comprising an average of 14 participants. An economic evaluation within the trial will be conducted to estimate the cost and cost-effectiveness of integrated community care compared with integrated facility care. This will be complemented by a built-in social science process evaluation. Ethics and dissemination Ethical approval was granted by the Research Ethics Committees of the University College London (UCL), the National Institute of Medical Research (Tanzania), and the Uganda Virus Research Institute (Uganda). The findings will be disseminated through journal publications and meetings with key stakeholders. Trial registration number ISRCTN Registry: ISRCTN15319595, registration date: 07 June 2022.