Monotonous rice-wheat cropping system with conventional management practices have resulted in declining soil quality and biota in addition to low input factor productivity and farmer’s profitability in western Indo-Gangetic plains (IGP) of India. Conservation agriculture (CA) based sustainable intensification (SI) is required to improve the soil quality while improving the productivity and profitability. A field experiment was conducted to evaluate the effects of CA based management practices such as zero tillage (ZT), direct seeding of rice (DSR), crop diversification, residue recycling and legume integration for SI in comparison to conventional management on soil quality and biota in cereal (rice and maize) based cropping systems. Fourteen treatments were included in which four treatments (T1–T4) with rice–wheat and two treatments (T11–T12) with maize-wheat system were based on conventional management, while six treatments (T5–T10) with rice–wheat and two (T13–T14) with maize-wheat were based on CA management practices. Conservation agriculture based SI of maize-wheat-mungbean (T14) recorded lower soil bulk density (1.33 Mg m−3). Soil organic carbon (OC) was increased by 83% and 72% with CA based rice-wheat-mungbean (T10) and maize-wheat-mungbean (T14) system, respectively and it was at par with T9 and T12 compared to farmer’s practice (T1) (4.6 g kg−1). Mean microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN) were 213% and 293% higher with T14 over T1 (646 and 201 μg g−1 dry soil), respectively. However, T10 recorded 117% and 171% higher MBC and MBN, respectively compared to T1. Dehydrogenase activity (DHA) and alkaline phosphatase activity (APA) were improved by 210% and 49% under T14; 140% and 42% under T10 compared to T1 (180 μg TPF g−1 soil 24 h−1 and 144 μg p-nitrophenol g−1h−1), respectively. Mean number of bacteria, fungi and actinomycetes were increased by 28%, 68%, 98% respectively, under T14 relative to T1, and at par with T12 and T10. Most abundant micro-arthropod group belonged toCollembola followed by Acari and Protura, irrespective of treatments. Higher soil quality index (SQI) was observed in T10 (0.82), followed by T14 and T6 treatment (0.76). Sustainable intensification of rice and maize based systems (T10 and T14) recorded 39% higher system yield compared to T1 (11.12 Mg ha−1). CA-based sustainable intensification of rice/maize systems improved soil quality and biota, hence resulted higher system yield in alluvial soils of IGP. Conservation agriculture based SI of maize-wheat-mungbean system was found to be the best alternative option than rice–wheat system to achieve sustainable productivity while improving the soil quality index (35%) and conservation of natural resources.