Innovative enterprises have a key role in the recognition and the sustainable development of the knowledge-based economy. The different innovative enterprises have different contribution and value for the economy and the social development. The R&D personnel and its acquired and developed competencies are basic characteristics of the innovative firms. On the base of the R&D personnel’s competencies a company competency profile is designed. This model may improve the innovation activity and the organizational performance of the enterprise. It can be used for making differentiation between innovative enterprises and on is base to be delivered conclusions on their competency competiveness. The competency profile can be useful for choosing what kind of innovations to be produced and in what innovate projects the company may participate. These innovative projects need concrete and specific competency tools. The competency profile works within a framework for improvement of the whole competency management of the innovative enterprise and introducing the best performance management practices for the R&D personnel.