INTRODUCTION: Sub-Saharan Africa continues to experience a syndemic of HIV and non-communicable diseases (NCDs). Vertical (stand-alone) HIV programming has provided high-quality care in the region, with almost 80% of people living with HIV in regular care and 90% virally suppressed. While integrated health education and concurrent management of HIV, hypertension and diabetes are being scaled up in clinics, innovative, more efficient and cost-effective interventions that include decentralisation into the community are required to respond to the increased burden of comorbid HIV/NCD disease. METHODS AND ANALYSIS: This protocol describes procedures for a process evaluation running concurrently with a pragmatic cluster-randomised trial (INTE-COMM) in Tanzania and Uganda that will compare community-based integrated care (HIV, diabetes and hypertension) with standard facility-based integrated care. The INTE-COMM intervention will manage multiple conditions (HIV, hypertension and diabetes) in the community via health monitoring and adherence/lifestyle advice (medicine, diet and exercise) provided by community nurses and trained lay workers, as well as the devolvement of NCD drug dispensing to the community level. Based on Bronfenbrenner's ecological systems theory, the process evaluation will use qualitative methods to investigate sociostructural factors shaping care delivery and outcomes in up to 10 standard care facilities and/or intervention community sites with linked healthcare facilities. Multistakeholder interviews (patients, community health workers and volunteers, healthcare providers, policymakers, clinical researchers and international and non-governmental organisations), focus group discussions (community leaders and members) and non-participant observations (community meetings and drug dispensing) will explore implementation from diverse perspectives at three timepoints in the trial implementation. Iterative sampling and analysis, moving between data collection points and data analysis to test emerging theories, will continue until saturation is reached. This process of analytic reflexivity and triangulation across methods and sources will provide findings to explain the main trial findings and offer clear directions for future efforts to sustain and scale up community-integrated care for HIV, diabetes and hypertension. ETHICS AND DISSEMINATION: The protocol has been approved by the University College of London (UK), the London School of Hygiene and Tropical Medicine Ethics Committee (UK), the Uganda National Council for Science and Technology and the Uganda Virus Research Institute Research and Ethics Committee (Uganda) and the Medical Research Coordinating Committee of the National Institute for Medical Research (Tanzania). The University College of London is the trial sponsor. Dissemination of findings will be done through journal publications and stakeholder meetings (with study participants, healthcare providers, policymakers and other stakeholders), local and international conferences, policy briefs, peer-reviewed journal articles and publications. TRIAL REGISTRATION NUMBER: ISRCTN15319595.