Background The number of people living with multiple chronic conditions in sub-Saharan Africa is increasing, but health facilities are unable to meet demand. To improve health system capacity and access to care, community models of HIV care have been trialled in countries such as Tanzania and Uganda. However, no evidence exists to inform policymakers on the effectiveness and cost-effectiveness of integrated community-based models of care for HIV and chronic non-communicable conditions. This protocol outlines a within-trial economic evaluation to address this gap. Methods & analysis We will estimate the costs and cost-effectiveness of integrated community-based care for HIV, hypertension and diabetes compared with facility-based care within the INTE-COMM pragmatic cluster-randomised trial in Tanzania and Uganda. Analyses will adopt a 52-week time horizon, the duration of trial follow-up. The full enrolled trial sample will be analysed from a societal perspective, comprising provider and patient perspectives. Economic costs will be estimated, which includes valuing inputs such as donated goods or time foregone by participants because of receiving care. For provider costs, participant case report forms will inform resource use along with data from facilities and community sites. Resources will be valued using project accounts, facility spending, and locally available cost data. Patient costs will be estimated based on a care-seeking and cost questionnaire administered to participants. Estimated costs will be analysed with co-primary trial outcomes on plasma viral load suppression, glycaemia and blood pressure control to calculate incremental cost-effectiveness ratios (ICER). We will also calculate ICERs for secondary trial outcomes related to health-related quality of life and wellbeing. Cost drivers and outcomes will be varied within confidence bounds in a two-way sensitivity analysis. We will investigate equity impact by estimating the mean difference in outcomes between integrated community-based and facility-based care across household socio-economic quintiles and by measuring whether participants incurred catastrophic health expenditures. Trial registration number The ISRCTN Registry: ISRCTN15319595. Registered on 07 June 2022: https://doi.org/10.1186/ISRCTN15319595