The sustainability of rice–wheat cropping system (RWCS) is threatened by increasing labor, water, and energy crises in the region. Conservation RWCSs offers an ecofriendly alternate option. This study was aimed to evaluate the impact of sesbania brown manuring in direct-seeded aerobic rice (DSAR) and of rice residue mulch in no-tilled wheat (NTW) on soil health, weed dynamics and system productivity. The experiment was composed of five RWCS systems: (i) DSAR-NTW; (ii) DSAR + sesbania brown manuring-NTW; (iii) DSAR-NTW + rice residue mulch; (iv) puddled transplanted flooded rice (PudTR)-NTW; and (v) PudTR-plow-tilled wheat. Sesbania brown manuring in direct-seeded rice decreased the weed density and dry biomass 41–56% and 62–75%, respectively, than the sole direct-seeded rice crop. At rice harvest, better soil health, in terms of total nitrogen (N), soil organic carbon, soil microbial biomass carbon, and soil microbial biomass nitrogen, was noted with DSAR + sesbania brown manuring-NTW. Rice residue mulch retention in NTW decreased weed density and dry weight by 60 and 69%, respectively, than those under NTW with no mulch. At wheat harvest, highest total N, soil organic carbon, and soil microbial biomass carbon were recorded with DSAR-NTW + rice residue mulch, followed by DSAR + sesbania brown manuring-NTW. Overall, NTW grown after DSAR + sesbania brown manuring produced more grain yield than PudTR-NTW and PudTR-plow-tilled wheat systems. In conclusion, sesbania brown manuring in DSAR and residue mulch retention in NTW may be opted to improve soil properties, suppress weeds, and to harvest better grain yield and achieve higher system productivity in conservation RWCSs.