ABSTRACTIn a changing climate, conservation tillage and agronomic biofortification are essential for enhancing crop yield, nutritional security, carbon stocks, and soil quality. Consequently, a field study was conducted in central India to assess the short‐term (4 years) effects of crop establishment techniques (CETs) and agronomic biofortification methods (ABMs) on soil health indicators, grain yield, and quality in the soybean–wheat cropping system. The experiment followed a split‐plot design with two CETs in the main plots (permanent broad bed furrow, PBBF, and conventional tillage, CT) and eight ABMs, each with three replications. The results indicated that PBBF and ABMs (seed inoculation with the microbial strains MDSR 14 + MDSR 34, and soil and foliar application of Zn+Fe) improved soil carbon stock (by 49.6% and 52.4%), available nitrogen, phosphorus, potassium, available Zn (by 30.0%), and Fe (by 21.9%) after the fourth year of the study. Similarly, PBBF and microbial inoculation increased soil enzyme activities (dehydrogenase, acid phosphatase, and β‐glucosidase), substrate‐induced respiration, and microbial biomass carbon content. As a result, a higher soybean equivalent yield (5.59% higher in PBBF and 14.2% higher with foliar spray of Zn+Fe) and seed quality attributes (crude protein yield, grain Zn, and Fe) were observed in PBBF and the foliar spray of Zn and Fe treatments compared to CT and control, respectively. Overall, adopting the short‐term PBBF system, microbial inoculation, and soil and foliar application of Zn and Fe improved rhizosphere biochemical properties, yield, and seed quality in the soybean–wheat system.