The intensive cultivation and multi nutrient deficiencies in trans-gangetic plains of India are affecting productivity potential of coarse textured, fine textured and salt affected soils which make it essential to appraise the novel soil quality indicators. The present study was carried out to analyze the variations in 36 bulk soil samples in texturally different and salt-affected soils under rice–wheat cropping system. Among soil properties, the average value of electrical conductivity (dS m−1), soil organic carbon (%), exchangeable sodium (%), available nitrogen (kg ha−1), available phosphorus (kg ha−1), available potassium (kg ha−1), available sulphur (mg kg−1) and DTPA-iron, manganese, zinc and copper (mg kg−1) were 1.58, 0.67, 10.7, 208, 85.4, 502, 32.3, 15.5, 5.29, 2.88, and 1.38, respectively. In soil quality index, 6 indicators in coarse textured, 5 in fine textured and 6 in salt affected soils explained the total variance of 90.5, 90.2and 93.7%, respectively. In overall, 6 indicators i.e. soil organic carbon, sulphur, carbonate + bicarbonate, soil pH, calcium + magnesium and manganese were identified as novel soil quality indicators under rice wheat cropping system of trans-gangetic plains of India.