The separation of proteins from olive oils by CE has been achieved for the first time in this work. Based on the protein profiles obtained using UV detection, a novel approach has also been proposed enabling the differentiation of monovarietal olive oils. An extraction procedure based on the precipitation of proteins in cold acetone and their isolation and solubilization in a hydro-organic medium prior to their in-capillary preconcentration in CE was a critical step in method development since proteins are minor components of olive oils. Then, a CE separation using a basic medium in a dynamically coated capillary originated electrophoretic profiles with multiple peaks from which seven of them were identified as proteins. When different monovarietal olive oils were injected, three different regions (zones I, II, and III) were identified. Zone III, called as differential zone, enabled to distinguish easily between extra virgin olive oils made from the Arbequina variety and the Picual and Hojiblanca varieties. This is the first time that protein profiles have been employed for the differentiation of botanical varieties of olive oils showing an enormous potential as traceability markers for these highly appreciated oils.