The Protestant Hospital offers three main areas of care. The University Clinics for Neurosurgery and Neurology cover the entire spectrum of neurological and neurosurgical diseases in interdisciplinary cooperation with the Institute for Radiology and Neuroradiology, the Clinic for Internal Medicine, the Clinic for Anaesthesiology and the Clinic for Interdisciplinary Intensive Care Medicine. The Evangelical Hospital also has a certified "supra-regional stroke unit". The close interdisciplinary integration of these clinics together with the Clinic for Trauma Surgery, Orthopaedics and Sports Traumatology enables the second focus of care as a certified "supra-regional trauma centre", which is also admitted to the German Social Accident Insurance Institutions' serious injury procedure (SAV). This makes the Protestant Hospital one of only nine clinics in Lower Saxony with unrestricted admission to treat severely injured patients.

The Clinic for Early Neurological Rehabilitation, which specialises in rehabilitation and palliative care and is actively involved in the Oldenburg Research Network for Emergency and Intensive Care Medicine (OFNI), is an important specialist addition. Other specialist areas include the diagnosis and treatment of neurological diseases such as dementia/Alzheimer's, multiple sclerosis, Parkinson's disease and epilepsy, brain tumour surgery and the treatment of tumours of the head and neck area as well as the treatment of hearing disorders using implantable hearing systems (cochlear implants). This audiological and ENT expertise represents the third clinical and scientific focus of care at the Protestant Hospital, which in turn can only be provided through close interdisciplinary cooperation with the other specialist departments based at the hospital.