Soil degradation associated with tillage is a major problem in Uruguayan agriculture. Either rotation of crops with pastures (ROT) or no-till (NT) cropping have been proposed as alternatives to minimize the impact of agriculture on soil quality. The combined impact on soil properties of ROT and NT has not been evaluated. In this study, we report results of the first 12 years of a long-term experiment established on a clay loam soil in western Uruguay. The objective was to determine the influence of conventional tillage (CT) and NT on systems under continuous cropping (CC, two crops per year) or ROT (3.5-year annual crops/2.5-year pastures). Soil samples taken at the beginning of the experiment in 1994 and in 2004 were analyzed for organic carbon (SOC), total organic carbon (TSOC) and total nitrogen content (STN), and for water-stable aggregation (WAS). Soil loss and erodibility indicators were studied using microrain simulator. With 12 years, the cumulative carbon (C) inputs of aboveground biomass were similar between tillage, but C input in CC was 50% higher than ROT. This difference was explained because 84% of the pastures dry matter was consumed by animals. Nevertheless we estimated a higher below ground biomass in ROT compared to CC systems (24.9 Mg ha-1 vs. 10.9 Mg ha-1). NT presented 7% higher SOC than CT (0-18 cm) with no differences between rotation systems. While all treatments declined in STN during 12 years, ROT had 11% and 58% higher STN and WAS than CC systems, with a large impact of the pasture under CT. Runoff and erosion were minimized under NT in both rotations systems. Thus, including pastures in the rotation, or switching from CT to NT improved soil quality properties. The expected benefit of combining NT and ROT will likely require more years for the cumulative effect to be detectable in both C input and soil properties.