Climate mitigation and adaptation planning (CMAP) has recently been implemented across the EU-28 to reduce GHG emissions (CO2, CH4, N2O). Thus, the aim of this study was to provide an overview of GHG emissions from the agricultural sector in the EU-28 from 1990 to 2019, and cluster the EU-28 countries regarding their total GHG emissions. The results emphasize the positive impact of CMAP through a negative trend of the total GHG emissions (−2653.01 thousand tons/year, p < 0.05). Despite the positive and not significant trend of the total CO2 emissions, both CH4 and N2O exhibited a negative and significant trend. At the country scale, Italy, the United Kingdom, and the Netherlands showed the highest reduction in total GHG emissions, by −282.61thousand tons/year (p < 0.05), −266.40 thousand tons/year (p < 0.05), and −262.91 thousand tons/year (p < 0.05), respectively. The output of the multivariate analysis approach indicates changes in the pattern of GHG emissions between 1990 and 2019, where CO2 emissions decreased in the case of Poland and Czechia. The output of this study highlights the positive impact of CMAP, adopted by EU countries, in minimizing GHG emissions. Despite some fluctuations in CO2 emissions, strategies for attaining carbon neutrality in the agricultural sector, across the European Union, should be pursued.