Soil quality issues have been researched within a crop rotation experiment that started in 1994 at Narrabri. It compares three crop rotations that have included or excluded legume phases throughout this period. The data presented here relate to the most recent 2-year cycle of this experiment. Following cotton harvest in all three rotation systems in May 2004, oats was sown in two systems. Following oat harvest, the soil was either left fallow (oat-fallow treatment) or vetch was sown in the April 2005 and green-manured in August 2005 (oat-vetch treatment). In the third treatment, vetch was planted in May 2004, green-manured in August 2004 and cotton sown in October 2004, vetch was sown in May 2005 and green-manured in August 2005 (vetch-cotton-vetch treatment). Cotton (cv Sicot 71BR) was sown in October 2005 across all systems.