This paper provides values of economic, energy and environmental assessments of 20 crops and assesses the relationships of soil-climatic conditions in the example of the Czech Republic. The comparison of main soil quality indicators according to the configuration of land and climate regions is performed on the basis of energy and economic efficiency as well as a comparison of the level of environmental impacts. The environmental impacts are identified based on the assessment of emissions from production and also in the form of soil compaction as an indicator of the relationship to soil quality. As concerns soil properties, of major importance is soil skeleton, slope of land and the depth of soil, which cause an increase in emissions from the energy produced. Substantially better emission parameters per 1 MJ through energy crops, the cultivation of perennial crops and silage maize has been supported. Among energy crops, a positive relationship with the quality of soil is seen in alfalfa, with a significant reduction in soil penetrometric resistance; energy crops are also politically justifiable in competition with other crops intended for nutrition of population. The main advantage of energy crops for the low-carbon economy is their CO2 production to MJ, which is almost half, especially in marginal areas with lower soil depths, slopes and stoniness, which can be included in the new agricultural policy.