While the market price of land in Czechia has increased in recent years, the officially set land price, published by the State Land Office and the Research Institute for Soil and Water Conservation, has decreased in several regions (Olomouc, Zlín, South Moravia, Moravian-Silesian, and Central Bohemia Region). Four out of five of these regions are said to have the most fertile soil. The main reason for the official land price decrease has been the re-evaluation of land parcels which are based on field sample testing. Based on these sample tests some parcels have been re-evaluated as less fertile. This paper aims to identify the main determinants, which led to the decrease of the official land price and soil fertility in these regions of Czechia. It has been determined that crop structure significantly differs from the “valuation type structure” which indicates optimal share of individual crops to achieve the optimal yield without soil degradation. It has also been determined that there were statistically significant differences in all selected regions for all observed crops (excluding rapeseed in Moravian-Silesian Region) and Czechia between the shares of individual crops and shares according to the “valuation type structure”. It may be concluded that farmers follow short-term interests (profit) instead of long-term goals (soil fertility) in the selected regions. Moreover, results for Czechia suggest that this trend is becoming more common in every region of Czechia. Thus, the Herfindahl–Hirschman Index was utilized. The Herfindahl–Hirschman Index shows decreasing crop diversity in all selected region, as in Czechia as well. Based on the data analysis, it is possible to identify several crops, which are prevailing (wheat, barley, rapeseed, and fodder crops). Three of these crops (wheat, barley, and rapeseed) in combination with intensive farming and poor crop rotation have been found to be problematic and a potential threat which may cause degradation in soil fertility. Based upon this the following measures have been recommended: First, to focus on proven agricultural practices, including crop rotation and fodder crops. Second, the fodder crops production should be supported, and the structure of the “single area payment subsidies” should reflect the negative impact of the three main prevailing crops (wheat, maize, and barley) on soil fertility and the decrease of livestock production in Czechia.