Organic farming is system with a growing interest worldwide. The objective of this paper was an assessment of the after-effects of perennial cultivation of spring barley, oats, and red clover in both conventional and organic systems on the chemical properties, enzymatic activity, and potential biochemical soil fertility index of the soil. The study analyzed the activity of acid phosphatase, alkaline phosphatase, urease and dehydrogenases as well as the potential biochemical soil fertility index of soil and the chemical parameters of soil. Soil material was collected from spring wheat grown after spring barley, oats and red clover, occurring in conventional or organic systems in 2009-2019. It has been shown that, compared to a conventional system, the perennial cultivation of red clover and cereals in the organic farming system has contributed to a significant improvement in the chemical (pHKCl by an average of 8%, total organic carbon – 18%, total nitrogen – 15%, N-NH4+ – 34%) and enzymatic (acid phosphatase – 29%, alkaline phosphatase – 67%, urease – 28% and dehydrogenases – 25%) soil quality indicators. The potential biochemical soil fertility index values were also significantly higher in soils in the organic farming system (by an average of 39%).