Innovative products and processes dictate the position held in the market by manufacturing enterprises. Effective innovation management and the stimulation of process and product innovations can support the development strategy of manufacturing enterprises. In this article, a model for innovation management system, (IMS) dedicated to an engineered-to-order (ETO) enterprise is presented. The system is integrated with an ERP database and includes a products and processes configurator. On the basis of the research conducted on innovative ETO enterprises, the authors have also elaborated a model for the development of new products within an ETO enterprise. To verify the usefulness of the model, a practical example of the implementation of an innovation management system within an ETO enterprise is given. The methodology for implementing an innovation management system in an ETO company is proposed.