Background: Integrated care is increasingly used to manage chronic conditions. In Uganda, the integration of HIV, diabetes and hypertension care has been piloted leveraging the well facilitated and established HIV health care provision structures. This qualitative study aimed to investigate the perceptions and experiences of patients, health care providers, clinical researchers, representatives from international NGOs, community members/leaders and policy makers on integrated management of HIV, diabetes and hypertension at selected government clinics in Central Uganda. Methods: We adopted a qualitative-observational design and participants were purposively selected. In-depth interviews were conducted with patients and with health care providers, clinical researchers, policy makers, and representatives from international NGOs. Focus group discussions were conducted with community members and leaders. Clinical procedures in the integrated care clinic were also observed. Data were managed using Nvivo 12 and analyzed thematically.Results: Triangulated findings revealed perceptions of integration reducing the frequency with which patients with comorbidities (HIV, diabetes, hypertension) visited health facilities, reduced the associated treatment costs, increased interpersonal relationships among patients and healthcare providers, and promoted capacity of health care providers to manage multiple chronic conditions. Integration also reduced stigma mainly through creating opportunities for health education, which allayed patient fears and increased their resolve to enroll for and adhere to treatment. Patients also had an opportunity to offer and receive psycho-social support and coupled with the support they received from healthcare workers, this strengthened the patient-patient relationship and provider-patient relationship, one of the building blocks of integration. Although, the integrated model significantly reduced stigma in general, it did not eradicate service level challenges and societal discrimination among HIV patients. Conclusion: The study narratives reveal that, in low resource settings like Uganda, integration of HIV, diabetes and hypertension care has potential to support patient experiences of co-morbid care. Integrated clinics may function as a central stigma mitigation strategy, operating independently of existing clinics and treating a range of conditions including HIV and other STIs.