In urban areas, land use usually increases soil degradation. However, there are areas occupied by agriculture and woodlands with an essential role in provisioning food and other services such as water and climate regulation. The objective of this work was to assess the effect of long-term land use and soil management practices on peri-urban soils in Zagreb (Croatia). Samples were collected at depth 0–10 cm within intensively tilled cropland (CROP) and vineyard (VINE), traditional grass-covered orchard (ORCH), and forest (FOR). The results showed that bulk density was significantly higher in VINE and CROP than in ORCH and FOR. The opposite dynamic was observed in water-holding capacity, air-filled porosity, aggregate stability, organic matter, and soil organic matter stocks (SOCS). Soil water infiltration was higher in FOR plot compared to the other plots. Overall, land-use change had a substantial impact on soil properties and SOCS, especially in CROP and VINE soils. Tillage, pesticides, and fertilizer applications were presumably the reasons for altered soil quality properties. Intensively used areas (VINE and CROPS) may reduce soil ecosystems services such as the capacity for flood retention and C sequestration.