Small and medium enterprises (SMEs) are a powerful economic force, significant employers, and creators of added value. In the European Union SMEs are the backbone of its economic and innovative potential, and for this reason, economic development and stability of SMEs are critical. The goal of this study is to apply modern controlling to the management of SME value growth using the tools and indicators of financial analysis. This study is based on a detailed analysis of 359 companies from the European Union in order to test 4 hypotheses. The data obtained were subjected to statistical analysis to identify the dependence between the controlling management of a company, tools of financial analysis, innovative potential, level of digitization, internal auditing, and HR communication tools used in the SME. The statistical analysis confirmed a close relationship between the studied variables and created a model for managing the company’s value growth for the study sample of SMEs. Subsequent experimental testing was used to confirm these conclusions, and other important associations were found that are important for successful management of SMEs value growth. The findings obtained are applicable in practice and can be used for a deeper analysis of the issues in question.