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People with COVID-19 may experience physical, cognitive, and psychological problems. Many cases are living with chronic symptoms even after recovery, such as impaired physical functions, brain fog, and depression. The Hong Kong Rehabilitation Programme for COVID-19 develops a new paradigm for patient rehabilitation needed now and in the future. A 12-week programme with tele-exercise and Chinese herbal medicine, both individually as well as combined, will be provided to around 200 registered recovering COVID-19 patients. As per our knowledge, this programme would be the first of its kind of experimental intervention using a combination of exercise and Chinese medicine and exploring the role of the gut microbiome to study the rehabilitation of COVID-19 patients. It will help us understand how effective interventions could be implemented to enhance the quality of life and mental health of the recovering patients. It will also shed light on how Chinese herbal medicines, gut microbiome, and its metabolites regulate immune function, intestinal permeability, and possibly autoimmune deficiency (AID) in the pathological recovery/rehabilitation process. We expect this 12-weeks long exercise or Chinese medicines to help patients recover from virus-induced chronic conditions and return to  healthy living.