Different management systems, including quality management systems, are widely used in enterprises and organizations nowadays. The procedure for establishing and effectively using quality management systems is regulated by the system of national standards. At the same time, the approaches to organization and the performance of quality management systems in enterprises depend on the personnel’s training, knowledge and understanding of existing regulations in the field of standardization and technical regulation. The main problems of effective quality management using quality management systems arise from inept application of existing regulations and a formal approach to organization and management of quality management systems. This primarily happens due to lack of involvement of the staff, lack of understanding of the role and responsibility of the process owner. Ensuring the required quality of processes is achieved by hiring competent managers and specialists for the enterprise. This means that human resources are sufficiently prepared, with a quality system of motivation and a high corporate culture. The company has created a system of information support, electronic document management system. In many enterprises, QMS documents are maintained by quality services, which are perceived as units solely responsible for maintaining the quality management system in working condition. Unfortunately, the functions of quality services are often limited to maintaining the QMS documentation in working order. However, all units of the enterprise must have the required documentation for the QMS available and keep the records prescribed by the QMS documents, the employees should know the contents of QMS documentation, have the skills necessary for document management. A formal approach to quality management systems in enterprises means that the resources allocated to maintaining the management system are used inefficiently. The article gives a brief analysis of the specific problems arising in application of quality management systems and the main directions for eliminating non-compliance of systems with the requirements of federal legislation and normative documents in the field of standardization. We have emphasized that the basic principle of building a quality management system in the enterprise should be the adapting the system to the needs of the enterprise while complying with the national standards of the Russian Federation. This paper presents a generalized view of scientists and specialists on actual problems encountered in implementing QMS in enterprises. We have proposed specific practical solutions (recommendations) formed on the basis of practical construction and application of the QMS.