Transformations in agriculture not only change the ways in which natural resources and social capital are used but are also a prerequisite for different opportunities to create added value and improve the viability and sustainability of rural areas. The purpose of this article is to assess the differences and effects of transformations in agriculture in the Bulgarian regions. Based on statistical data from the Censuses of agricultural holdings in 2010 and 2020, the DEA method was applied. Six models (three input-oriented and three output-oriented) were constructed and tested, and the efficiency coefficients were assessed on a regional level. The degree of structural changes and the efficiency of the used production and other resources were evaluated, and conclusions were drawn. In the majority of the models, differences were observed between the Northern regions of the country and the South Western and South Central regions. The most significant are the efficiency coefficient of the labor force used, and the output produced, the gross value added, and the net mixed income. In the other models, multidirectional changes were observed. The North Western is the region in which all calculated efficiency coefficients increased, and in the North Eastern and South Eastern regions, the most calculated coefficients decreased. Based on the analysis, recommendations related to region-specific agricultural policies for better resource allocation and sustainable development are proposed.