Defining the balance between socio-economical and bio-physical aspects in order to promote sustainable development in agriculture is a fundamental challenge for researchers. The aim of this study is to assist in constructing a science of sustainability in agriculture and to assess sustainability in various types of agroecosystem managements characterized by different agricultural and rural developments. This study evaluates sustainability on Terceira Island (Portugal) and in the Province of Viterbo (Italy) by using selected agroecosystem sustainability indicators capable of achieving an energetic and monetary input/output analysis. Overall, results showed two rural and agricultural realities that outline two different responses to world market demand, which are partly due to specific rural histories. In terms of energy supply, Terceira and Viterbo dairy farms use the same amount of input but in monetary terms the level of input is more than double in Viterbo (€1651 ha−1 versus €616 ha−1) which is due to the lower cost of direct energy (e.g., fuel) on the island. The use of direct energy input (fuel, electricity and lubricants) on the farms in Viterbo decreases in mixed farm systems and is at its minimum on dairy farms. On the other hand, the use of indirect energy input (fertilizers, herbicides, pesticides, seeds and feedstuffs) is greater on Terceira farms compared with those in Viterbo (0.76 versus 0.60, respectively). Generally speaking, the crops grown on Terceira are not diversified and this has caused environmental issues on the island due to the milk production that is mainly exported. In Europe, more intellectual and financial resources for measuring and monitoring sustainability conditions in agriculture are necessary, in order to appropriately inform decision makers at both institutional and individual level.