The European Green Deal sets an ambitious target for Europe to reach climate neutrality by 2050. This commitment will be a challenge, particularly in the context of agriculture, as the sector is responsible for sustainable development and food security. However, one of the primary sources of GHG emissions from the agricultural sector is the treatment of soils using nitrogen fertilizers for crops, especially grain crops. This paper aims to assess the GHG mitigation perspective for soil management in the Baltic States and, in particular, to analyse the grain sector in light of sustainable agriculture and towards climate neutrality. To achieve the aim of the study, the analysis was performed in two parts. Firstly, historical and projected GHG emissions of the Baltic States and mitigation measures on agricultural soil management, including cereal growing were analysed as these emissions show a growing tendency. Thus, the study analyses GHG emission trends, including possible mitigation measures for soil management in the Baltic States. The results indicated that for GHG reduction from agricultural soils, some cost-effective measures could be considered for the future, such as the zero-emissions on-farm machinery and equipment, low or no-tillage, or N-inhibitors on pasture. Secondly, as the GHG emissions from cereals increase, potential alternatives to the use of grain production have been explored to assess the highest possible added value from the product use, thus also contributing to GHG reduction. In this regard, according to scientific literature, a survey was created in the form of a questionnaire based on 32 alternatives, 4 large product groups, and 4 criteria for cereal and straw processing. The respondents were requested to provide an assessment of alternatives, and consequently, a multi-criteria decision analysis (MCDA) was performed using the TOPSIS method. The results reveal the best alternatives from each of the product groups consequently is flour from food products, minerals from a pharmaceutical, biogas from a form of transport and reusable tableware from straw-based products, as a possible cost-effective mitigation measure for soil management from the perspective of the development of sustainable agriculture sector and the transition towards climate neutrality.