Doctors who use biomedicine with complementary and alternative medicine (CAM) in a carefully integrated way offer benefits from both systems to chronic patients without compromising on safety. The Institute of Applied Dermatology, Kasaragod has successfully developed a model of integrative medicine (IM) and effectively managed lymphoedema patients. This article describes the process of developing IM treatment adopting 'standard protocol items and recommendations for interventional trials'. All patients were examined by a team of doctors, biomedical and CAM, and nurses, thus enabling each patient's condition to be understood from these different perspectives, and diagnosis and management through an IM approach. A minimum of 30 min counselling is essential for every patient before informed consent is gained. The 'systems-based' conclusive process follows the standard guidelines in each therapeutic discipline. IM management is achieved following 'bedside discussion'. The minimum requirements for a clinical setting to conduct IM studies, documentation, patient selection and follow-up are described, utilizing biomedical outcome measures to demonstrate the effectiveness of IM. Components of the IM case record algorithm are described here. The process of clinical examination for Ayurveda is described along with comparative biomedical explanation. Biomedical confirmatory study, maintaining records of primary outcome measures, transcription of IM discussions and follow-up entries of patients under IM are also explained. Improving IM protocols for patient care has involved input from global experts together with feedback from patients who have received IM treatment. The IM treatment protocol should evolve as a patient-oriented approach. The protocol discussed here focuses on biomedical systems and structures to measure its effectiveness. This article provides a method for conducting evidence-based clinical studies to develop new IM therapies for chronic skin diseases.