Properly chosen soil management practices can stabilize the nutrient regime in the soil, including the mobility and bioavailability of hazardous elements. This study aimed to identify the optimal soil management practices in a productive vineyard on Rendzic Leptosol in the Nitra wine region (Slovakia). Soil samples were collected each spring from two depths, 0–30 cm, and 30–60 cm, with the following treatments: T—soil tillage, P + FYM—plowed farmyard manure, G—grass strips, G + NPK1—first-level fertilization, and G + NPK2—second-level fertilization, from 2019 to 2023. The results indicated that more pronounced changes in soil properties occurred in the 0–30 cm layer. Higher NPK rates significantly affected soil sorption capacity and decreased soil pH when compared to other treatments. While G + NPK2 showed the highest storage of total N, S, P, K, and available P and K, it exhibited the lowest levels of total and available Ca. The T treatment displayed the lowest storage of C, N, S, P, and available K. In terms of hazardous metals (Cr, Ni, Pb, and Zn) none exceeded the limiting values in any of the soil management practices. However, in the 0–30 cm layer, Cu concentrations exceeded the limits set by Slovak Republic regulations in the T, P + FYM, G, G + NPK1, and G + NPK2 treatments by 62.6, 73.7, 70.2, 82.1, and 102.9 mg kg−1, respectively. Additionally, as total C increased, Cr concentration was observed to decrease with correlation (r = −0.46). Positive correlations were found between total C and Zn, as well as CaCO3 and Zn in the 0–30 layer.