Aim: To explore the perceived barriers and facilitators in the management of the patients having diabetes with comorbidities by primary care physicians. Methods: A qualitative In-Depth Interview study was conducted among the primary care physicians at seventeen urban primary health care centres at Bhubaneswar city of Odisha, India. The digitally recorded interviews were transcribed verbatim and translated into English. The data were analysed using thematic analysis. Results: Barriers related to physicians, patients and health system were identified. Physicians felt lack of necessary knowledge and skills, communication skills and overburdening due to multiple responsibilities to be major barriers to quality care. Patients’ attitude and beliefs along with socio-economic status played an important role in treatment adherence and in the management of their disease conditions. Poor infrastructure, irregular medicine supply, and shortage of skilled allied health professionals were also found to be barriers to optimal care delivery, as was the lack of electronic medical records and personal treatment records. Conclusion: Comprehensive guidelines with on the job training for capacity building of the physicians and creation of multidisciplinary teams at primary care level for a more holistic approach towards management of diabetes with comorbidities could be the way forward to optimal delivery of care.