Soil plays a key role in sustainable land management and food production. The objective of the field experiment was to evaluate the subsequent effect of 10-year winter wheat and sugar beet cultivation under conventional and organic systems on selected physicochemical and biochemical properties and enzymatic pH index of lessive soil developed from loess under climatic conditions of Southeastern Poland. The experiment was set up by using the split-plot design, with three replications, on plots of 30 m2. In order to evaluate the soil value of sites cultivated in 2010–2019 in two systems—conventional agriculture and organic agriculture—spring wheat was sown as a test crop in 2020. Fertilization and pesticide applications (herbicides, fungicides and insecticides) were foregone in the cultivation of this crop due to the desire to capture the subsequent impact of 2010–2019. This resulted in soil properties shaped solely by the previous 10 years of cultivation. The obtained results indicate that the organic farming system contributed to the improvement of soil pHKCl compared to the conventional system, with statistically significant differences recorded only for winter wheat cultivation. Compared to the conventional system, in the organic farming system, improvements were recorded in the chemical indicators of loess soil quality (TOC, TN and TOC/TN) and P content, as well as acid phosphatase and alkaline phosphatase activities. However, statistically significant differences were found only for winter wheat cultivation. Research on the impact of an organic system of growing different species in rotation should be continued, and the results should be implemented