Providing food security while preserving natural resources and reducing the use of production factors (land, labor, and capital), is a critical challenge for EU agricultural sectors in the 21st century. Sustainable Development goals adoption has increased the need for eliminating Greenhouse gas emissions across all EU sectors, while production should remain stable or even increase. For this purpose, Window Data Envelopment Analysis (DEA) has been selected as a benchmarking technique, in order to assess input use efficiency of agricultural sectors of EU countries for the 2005–2019 period. Moreover, three-year projections (until 2022) have been calculated in order to acquire future efficiency scores. Emphasis has been given on the selection of alternative window widths, examining their influence on calculating efficiency scores for both projected and actual dataset. From a methodological point of view, this paper aims to highlight the assumption of zero technological change within Window DEA frames and present their differences. At the same time, results indicate that Estonia (1.000), the Netherlands (0.999) and Slovenia (0.999) are the most efficient countries in terms of input use efficiency, while Finland, UK, and Hungary (0.670, 0.755 and 0.771) score the least. Countries of central Europe (Hungary, Czech Rep., Croatia, Slovakia, and Austria) should redesign their agricultural strategies, so as to achieve the nine objectives of the upcoming CAP (2021–2027).