This contribution is devoted to the study of 125 innovative-oriented companies of the MSME (Micro, small and medium enterprises) complex. The research purpose is to develop a methodology for configuring MSME management systems in conditions of turbulence. For 5 years, the authors conducted a deep interview with the owners and management of companies. We collected data on the tools used and methods of management theory, as well as about the problems that the owners of innovation-driven enterprises (IDE) face when building a management system in a turbulent environment. During the study, the authors relied on the case study methods and the grounded theory method forming the concept of configuring control systems. The results of the analysis of the collected data and the conclusions obtained by the authors are presented in the final section of this work. One of the limited resources for the founders of IDE companies is time, which affects the insufficient development of management theory by owners, who are most often managers of their business. This affects the quality of the control system they created, which does not withstand turbulence, does not meet the requirements of the flexibility and stability that are necessary for the regular development of innovations. The work presents an authors’ concept that develops the direction of configuration management, but focuses not on a static configuration, but on the methods of regular transformation of the management system, dynamic configuration.