Soil quality integrates the effects of soil physical, chemical and biological attributes. Some of them are dynamic in nature and behave differentially in various agro-ecosystems (AESs) and are quantified in terms of a soil quality index (SQI). An attempt has been made in this paper to develop an SQI based on a minimum data set (MDS), which could be used to evaluate the sustainability of the crop production in three varying AESs in India, namely sub-humid, semi-arid and arid. Thirteen indicators were utilized to develop the SQI from the properties measured from the surface soil layer (0–15 cm). Each indicator of the MDS was transformed into a dimensionless score based on scoring functions (linear and non-linear) and integrated into four SQIs. The weighted non-linear index (WNLI) was identified as the most sensitive for all the AESs and was recommended as an index for future assessments. Based on this index, the quantification of soil quality under several cropping systems was carried out for sub-humid, semi-arid and arid AESs and the most suitable cropping system was identified. WLNI was positively and significantly correlated (R2 = 0.79, p < 0.01) with wheat equivalent yield for all the cropping systems. This clearly indicated that the index may be used satisfactorily for quantifying soil quality.