Soil quality indicators (SQI) can be used as a synthetic tool for the assessment of the sustainability of agricultural systems. In this study, we developed SQI using minimum data set (MDS) and determined the response of SQI to long-term tillage systems. Field pea (Pisum sativum L.) and spring wheat (Triticum aestivum L.) were grown in alternate years at northwestern China, and soil attributes and crop productivity were measured 6 years after the initiation of the experiment. The MDS used to develop the SQI included soil physical (aggregate, bulk density, capillary porosity, field capacity), chemical (soil organic matter, total nitrogen, available phosphorus, available potassium) and biological (microbial count, microbial biomass, and the activities of catalase, urease, alkaline phosphatase, and invertase) properties. All the property variables were measured in each of the 0–5, 5–10 and 10–30 cm depths and those variables that contributed significantly to the SQI were selected to be included in the MDS. Amongst the measured variables, bulk density and microbial counts occurred in the MDS of all the three depths, suggesting that these two properties are highly affected by the tillage treatments. In the long-term field experiment, the no-till with stubble covering the soil surface treatment received the greatest SQI score and achieved the highest crop yield. Soil quality under tillage systems can be assessed adequately using MDS measured at the top soil (0–5 cm) layer in rainfed agro-ecosystems.