In the modern era, intensive agricultural practices such as agrochemicals are applied in excessive amounts to enhance agricultural production. However, imbalanced adoption of these chemicals has arisen in the dwindling of agriculture factor productivity and soil quality. To maintain soil fertility and production, these chemical fertilizers must be supplemented with organic inputs. Keeping this in the backdrop, a research trail was established during 2018–19 and 2019–20 years at Research Farm of Agriculture University, Kota, India. The treatment setup was comprised of 5 treatment modules viz., conservation tillage + organic management (CAOM), conservation tillage + chemical management (CACM), conventional tillage + chemical management (CTCM), conventional tillage + organic management (CTOM) and the package of practices (PoPs) with four replications. Results indicated that the highest organic carbon (0.68%), bacterial (29.11 × 107 cfu g−1), fungal (4.77 × 104 cfu g−1), actinomycetes populations (5.67 × 104 cfu g−1), acid phosphatase (44.1 µg g−1 h−1), urease (45.3 µg g−1 h−1) and dehydrogenase (23.3 µg triphenylformazan [TPF] g−1 h−1) activity in soil were found in the treatment of conservation organic system during both the years of study at each soil depth. In contrast to other parameters, the highest system productivity was observed with conservation chemical crop management approaches, with a soybean equivalent yield of 4615 kg ha−1 in a soybean–wheat system of production. Furthermore, the soil quality index (SQI) significantly varied from the lowest score (0.30) at 45–60 cm layer of soil in the package of practices to the highest score (0.92) at 0–15 cm layer of soil with regards to the conservation organic which shows, 206.67 percent enhancement through the soil profile of various crop management practices. The SQI variation from 0–15 to 45–60 cm soil depth was 130.0, 81.08, 60.0, 175.0 and 83.33 percent, respectively, for CAOM, CACM, CTCM, CTOM and PoPs. Amongst, different systems, the highest mean performance was noticed under the conservation organic systems for physical and biological properties. Hence, in line with the salient outcome, we may propose that the conservation chemical system needs to be followed to improve crop productivity, whereas, conservation organic seems a good option for soil health with long-term viability.