This paper evaluates the level of governance sustainability of major agro-ecosystems in Bulgaria, and its “contribution” to the integral sustainability of respective agro-ecosystems. Modern achievements of the theories of Sustainable Development and New Institutional Economics are incorporated, and a holistic hierarchical system of Principles, Criteria, Indicators, and Reference Values for assessing Governance and Integral sustainability of agro-ecosystems in Bulgarian elaborated and empirically tested. Assessment has found out that there is a considerable differentiation in the level of Governance sustainability of different agro-ecosystems in the country with the highest (“Good”) demonstrated by agro-ecosystems with “Lands in protected zones and territories” and those in “Less-favored mountainous” regions, while agro-ecosystems “Mainly plain” and “Less-favored non-mountainous” regions are lowest and bellow national, second one being at Satisfactory level. Inclusion of the “Governance Pillar” affects unequally the Integral Sustainability of different agro-ecosystem. While for agroecosystem in “Less-favored mountainous” region calculations with and without governance pillar are almost the same, for other agro-ecosystems inclusion of the governance dimension decreases the overall sustainability.