Extended exergy accounting (EEA) is a methodology which estimates the extended exergy cost (EEC) of a product or a service or the extended exergy efficiency (EEE) of a country or economic sector taking into account materials, energy, labour, capital, and environmental impact. The use of EEA results for policy or planning purposes has been hampered by: (1) the lack of data to quantify the EEC of most of the inputs, making it almost impossible to quantify the EEC of a product or service and (2) the lack of a conceptual framework to quantify in a consistent way the exergy of labour and capital. In this paper, we make a review of past studies to identify, synthesize, and discuss the different EEA methods. We identified 3 different EEA methods, that we further compare using the Portuguese Agriculture, Forestry, and Fishery (AFF) sector from 2000 to 2012. The equivalent exergies of labour and capital estimated for the AFF sector vary widely among the three EEA methodologies. We propose and test a new EEA methodology to estimate EEE which accounts for these fluxes in a more restricted scope but more consistently and that includes the Environmental Benefit (EB) that represents the capability of the forestry to capture carbon dioxide. Results show that the EEE of the Portuguese AFF sector has increased by 32% from 2000 to 2012.