The paper studies the problems of non-profit organisations and their provision of social services in the processes of sustainable development and economic security of rural areas. The methodological basis of the research includes the theoretical positions of regional typology, sustainable development, regional and spatial economics, as well as approaches to the study of the effectiveness of non-profit organisations. The functioning of non-profit organisations, as well as the demand for social services, is revealed by using a combination of methods: dialectical, causal and ranking values of statistical indicators. The problems of rural development in agrarian-industrial regions are highlighted and the participation of non-profit organisations in solving these problems is substantiated. The authors emphasise the need to apply the mechanisms of programme-targeted management of rural development in the context of sustainable development processes and economic security.