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In this study, the impacts of long-term soil and crop management practices on crop productivity and soil health in oilseed brassica-based production systems were examined. Different tillage, crop residue recycling and cropping systems (fallow–mustard, cluster bean–mustard, green gram–mustard, maize–mustard, pearl millet–mustard and sesame–mustard) were studied for 5 years at two soil depths (0–15 and 15–30 cm) in a split-plot design with three replications. No-till permanent beds with crop residue (PB + R) noticeably improved soil organic carbon (SOC), microbial biomass carbon (MBC), enzymes (dehydrogenase (DHA) and alkaline phosphatase (AlP)), nitrogen fractions (available and total nitrate) and available phosphorus and potassium content in both soil layers compared to conventional tillage without crop residues. However, the plough soil layer (0–15 cm) showed higher concentrations of soil carbon, enzymes, N fractions and available P than in the subsoil (15–30 cm). The dynamic soil biological and chemical properties also varied with the crop stage, and higher MBC at 30 days, SOC and enzymatic activities at 60 days, and N fractions and available P and K during the harvesting of mustard crop were recorded. Green gram–mustard rotation showed higher values in terms of biological and chemical parameters. Thus, the legume-based mustard crop rotation following no-till permanent beds and residue recycling was found to be holistic in terms of improving soil health and nutrient cycling.