The aim of the paper is to formulate preconditions for the proposal of a methodology for the evaluation of innovative projects by SME (small and medium enterprise) management. It is about designing a comprehensive conceptual framework for creating model tools for a new generation of modeling organizational systems to achieve a qualitative radical generation leap in the quality of support for innovative innovation processes in business management. The ability to model organizational systems comprehensively, but in a simple way, is a necessary condition for systemic perception and effective management of modern business entities. The basic theoretical contribution lies in the extension of management theory with new principles and knowledge. The practical benefit is the creation of a framework guide for the design of a methodology for the evaluation of innovation projects by SME management, for the functioning and innovative development of the researched, representatively specified entity, in the form of an innovation and quality program.