Understanding how different tillage practices affect crop productivity and soil fertility is essential for developing sustainable agriculture systems. Here we investigated how no-till affected winter wheat yield and soil fertility after 13 years since its introduction in a clay and a loam soil compared to conventional ploughing, shallow tillage and minimum tillage. During the study period 2007–2020 the annual yield of winter wheat did not differ significantly among the four tillage treatments. However, the no-till showed the lowest relative annual yield and the largest yield variability. The quality of winter wheat grains was affected primarily by the soil texture than by the tillage treatment. A significant effect of tillage on the stocks of soil organic carbon, total nitrogen and exchangeable potassium and magnesium was observed only in the topmost 10-cm, where larger values were found for the three non-inversion tillage treatments. However, when the entire 50-cm deep soil profiles were evaluated, only non-significant differences in nutrient stocks were detected between tillage treatments. We observed a clear stratification of microbial biomass carbon along the soil profile with larger values in the topmost soil layers in the no-till and the non-inversion minimum tillage. Overall, our data indicate that even if the no-till may still be in a transition phase in terms of crop yield, its positive effects on soil organic carbon and microbial biomass are observable after 13 years. In addition, we underline as the minimum tillage appears, at least under the local conditions, as a very suitable practice providing multiple agronomic and environmental advantages.