Many companies recognize the need to innovate their product portfolio. The use of traditional methods and approaches to assessing the activities of an enterprise does not allow to identify the contribution of innovative departments to the overall result of the company.The purpose of the study is to develop a method for evaluating individual units involved in the development of new products. The paper identifies key assessment parameters that contribute to the consideration of three key groups of indicators: general characteristics of the innovative activity of departments, the effectiveness of working with new products and the achievement of the goals of the company's functioning. Specific parameters for each group of indicators are proposed, which makes it possible to evaluate the effectiveness of the development organizational structure. Based on the proposed metrics, an integral assessment was obtained and the procedure for its calculation was determined. In accordance with the strategy and priorities of the development of the enterprise, it is possible to determine weighting factors for each component and individual indicators. To adjust the activities of departments to achieve the goals set, the procedure for searching for control action is determined. Two control problems are considered with a sufficient amount of resources and their limitations. In the first case, the department has the opportunity to complete all the planned tasks with the available resources, respectively, the task becomes an optimization one with the search for the most effective way of implementation at the intersection of the sets of planned tasks and possible results. In the second case, it is required to ensure the minimum deviation at each point at the minimum step due to the distribution and use of resources. The possibility of using the developed method to dynamically assess changes in the efficiency of individual organizational structures is demonstrated using the example of three divisions of LLC "Kompaniya IMPRINTA" involved in the development of additive equipment and technologies, including extrusion 3D printers, materials and software. Based on the analysis of the dynamics of changes in the integral assessment of the divisions of LLC "Kompaniya IMPRINTA", the problems of their functioning were identified and directions for improving the efficiency of divisions were identified, such as the development of aemployee motivation system to increase the number of proposed development ideas by the product marketing department and the development of measures to reduce the share of work performed by the department operation of the product with the involvement of third-party companies.