In many areas, organic crop production systems have been shown to contribute to maintaining good soil condition. The organic production system has been recommended as an alternative to conventional agriculture. However, in order to recommend this practice in new regions, it is necessary to obtain information about its effects and consequences in local environmental conditions. The research was completed during 2016–2018 in Osiny (Lublin region, Poland) on a field experiment established 26 years previously in a Haplic Luvisol soil. The research was aimed at comparing the effects of long-term use of tilled soil with organic (ORG) and conventional (CON) crop production systems with those in non-tilled soil under permanent grass (PRG) as a control. This comparison was done on the basis of changes in the values of soil properties as follows: Total porosity (TP), total organic matter (OM), particulate organic matter (POM), humic substances (HS), water-extractable carbon (WEC), microbial biomass carbon pool (MBC) and dehydrogenase activity (DH). Soil samples were collected from experimental fields (each treatment 1 ha) under winter wheat and permanent grass each year from 0–5, 5–10, 15–20 and 30–35 cm depths. Over the three year study period, it was found that permanent grass and the organic crop production system contributed to increased soil OM, POM, HS, WEC and MBC contents and DH activity compared to the CON system, especially in the top soil layer, 0–5 cm. To obtain a clearer picture of soil quality change our study examined for the first time the metabolic potential index (MPI) as a ratio of dehydrogenase activity to the soluble organic carbon content. The MPI values confirmed the increase of metabolism in ORG soil as a consequence of management practices compared with CON soil. The obtained correlations showed strong mutual relationships within properties of the heterogeneous soil complex. The results show the positive effects of the ORG management system causing soil condition improvement which is based on organic fertilization, enriching the soil with a large amount of plant residues in creating positive changes in the soil quality in contrast to the CON system.