In order for the programs co-financed by European Union funds to run successfully, various projects are implemented in various sectors. The project implementation and monitoring processes are created in accordance with the requirements of the regulatory acts established by Latvia and the European Union. Non-compliance with the rules may result in the return of the granted EU fund co-financing. Processes introduced that do not comply with regulatory enactments may result in the occurrence of a risk of conflict of interest. In order for the implementation of the project to proceed efficiently, the company needs to implement high-quality processes. The aim of this paper is to analyze the quality system by using a process approach in order to develop improvement suggestions for the prevention of possible errors in the processes of preparing the project applications and progress reports. Research methods such as qualitative content analysis, Porter's "five forces analysis model", Work distribution structure, Process mapping, Value stream mapping and FMECA were applied for the assessment of the quality management system. Based on both the theoretical research and a case study of a Research and Experimental Development Company proposals are developed for processes, for the quality management system and for the integrated management system.