Intensive agriculture is the chief cause of soil degradation particularly in regions with low status of soil organic carbon (SOC) as in the semi-arid of southern India. In the quest of attaining sustainable crop yield and improved soil quality, conservation agriculture (CA) is being advocated and adopted globally including India. In this present experiment, CA was implemented to investigate the synergetic impacts of different tillage and weed management practices on soil quality (SQ) and system yield (SY), and to identify remunerative treatment combination (tillage – weed management) which can sustain SY and enhance SQ. Three tillage practices (main plots); T1:CT(C)-CT(M)-fallow(NSr), T2:CT(C)-ZT(M)-ZT(Sr) and T3:ZT(C) + SrR-ZT(M) + CR-ZT(Sr) + MS and weed control tactics involved (sub plots); W1-Chemical weed control, W2-Herbicide rotation (in alternative year), W3- Integrated weed management (IWM) and W4-Single hand-weeded control with cotton-maize-Sesbania rostrata cropping system over 3 years. A total of 40 soil variables were analysed at 60 days after sowing (DAS) and after harvest of maize (5th cropping cycle) and subjected to principal component analysis (PCA) in SQI CAL software to choose variables, minimum data set (MDS) and obtain a soil quality index (SQI). The following soil properties; SOC, silt, available Zn, Fe, soil potassium, nitrogen, pH, EC, soil C: N and CEC were selected as indicators based on correlations, calculated PCA and adept opinions on the texture and lime concretions of the experimental soil. The SQI was improved (62.09%) by the adoption of T3 in combination with W4 (T3W4) followed by T3 and W3-IWM (T3W3) combination. The system cotton equivalent yield (CEY) was significantly higher (4453 kg ha− 1) under T3 and W3-IWM (T3W3), while significantly lower system CEY was observed under T3 with W4 combinations (T3W4). So, considering both the system CEY and soil quality, T3 and W3-IWM was considered as the best treatment combination among all others for sustenance of both the soil and crop productivity in semi-arid conditions of southern India.