In today's dynamic environment, the Republic of Moldova, as a small country, has an emerging economy, facing contradictory processes related to overcoming the recession caused by the incomplete implementation of the proposed new standards. The aim of the study is to identify and substantiate the problems of the quality management systems of small and medium enterprises in the Republic of Moldova, which reduce their potential. The paper presents comparative analysis of international standards ISO 9001: 2008 draft of the new version of ISO 9001: 2015, identifies the advantages and role versions ISO 9001: 2015 in order to improve the competitiveness of small and medium enterprises. In order to increase the competitiveness of the economic units, it is necessary to change the attitude of their superior management towards the quality management system and the observance of the basic principles of labor in the "consumer market" paradigm. Creating a favorable environment for the implementation of this system in small and medium enterprises will contribute to diminishing the threats of national economic security in conditions of economic instability. These processes are aggravated by the global economic crisis. Ensuring the quality management system within the national enterprises will increase the national economic security that will enable us to accelerate the integration of the Republic of Moldova into the European Union.