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Research background: Small and medium-sized businesses are significant economic power and employer in the European Union. The modern globalized world, new technologies, and advanced connectivity bring SMEs a wide range of opportunities, but also threats. Increasing the stability and competitiveness of SMEs is one of the main goals of national governments and the EU. The research is based on personal research in SMEs, its experiences and backward testing of reached results. Purpose of the article: The aim of the paper is to analyze the possibilities the potential of using controlling as a managing tool of SMEs for increased competitiveness in the context of Industry 4.0 with an emphasis on innovations. Methods: The study is based on a detailed analysis of 341 SMEs from the Czech Republic obtained in the years 2017–2019. The data were analyzed using statistical methods such Pearson correlation, stepwise regression for the purpose of determining the relationship between the controlling management system of a company, its innovation potential, level of process maturity, number of employees, internal audit, financial stability and strategic plan. Statistical analysis confirmed the close relationship of the analyzed variables and backwards experimental testing of the statistical analysis conclusions defined critical factors in the area of people in an organization, usage of advanced information systems and Industry 4.0 technologies implementation. Findings & Value added: Those important areas were determined as essential for the successful development of SMEs, as well as the most significant threats in the Industry 4.0 environment. The information obtained is useful in practice and can be applied to a more in-depth analysis of the issues. The research findings are showing possible opportunities and treads for SMEs long term stability and development as well as ways to increase enterprise performance based on controlling management system.