This paper presents the possibility of applying Business Intelligence Tools in the analysis of the use of EU funds with the help of indicators of financial analysis of business of enterprises beneficiaries of EU funds. In the theoretical part, the historical development and methodological concept of the application of business intelligence in business are presented, business indicators of financial analysis are processed and their significance is explained. In the empirical part of the paper, the research was focused on the practical application of the software tool Microsoft Power BI in the identification of indicators of financial analysis of business that in enterprises, which are the beneficiaries of EU funds, have a positive deviation comparing to the average of the industry. The identification of these indicators was achieved with the help of the numerous possibilities of visualization of analysis results offered by the Power BI tool, while for more complex calculations the advanced possibilities of the tool with the help of the DAX programming language were used. Two hypotheses as well as the answer to the research question were tested in the observed set of 1044 companies. The results of the empirical part of the paper confirmed that it is possible with the use of Power BI tools to identify indicators that are most common in enterprises beneficiaries of EU funds and the expected correlation between companies and the quality of business measured through financial analysis indicators. A precondition has been created for a further development model which should serve to identify the capacities of the best companies in investment projects that can create added value and which can serve as a basis for future development strategies to increase the quality of individual projects and therefore increase the efficiency of used of EU funds.