In recent years, various methods and practices for improving the efficiency of business systems have enabled organizations to achieve significant operational results. However, their real impact on current competitiveness indicators of enterprises, such as TSR and EBITDA, is still unclear. Lack of quantitative assessment of effect from using specific tools (methods and practices) for increasing the efficiency of business systems does not allow to formalize the choice of their combination ensuring maximum effect for a particular organization, project and goal. In these conditions, developing an approach to assessing the effect of different tools for improving the efficiency of business systems seems to be an urgent scientific task. To solve this problem, we proposed an approach that is based on levers of influence on the TSR (Total Shareholder Return), which is constantly in the investors' attention and is an indicator of the organization’s effectiveness in terms of competitiveness and factors of business system development level. A distinctive feature of the proposed methodology is the approach to grouping the evaluated instruments depending on the logic of their practical application. To collect the initial data for the analysis, the expert assessment method was used on the basis of a specially developed questionnaire, which was filled out according to the results of the project. This questionnaire includes such information as a list of tools used, the level of development of the business system and the effect obtained. As a result, for the regression analysis, we used data from 170 questionnaires obtained from the results of projects implemented in various companies of a multi-industry holding. The analysis made it possible to obtain the coefficients of influence of various tools to improve the efficiency of the business system on such indicators as quality of activity, productivity, costs. The resulting more accurate estimate of the numerical values for using these tools can be further used to solve the mathematical optimization problem to determine their effective set when implementing a transformation project.