Field experiments were conducted to evaluate eight different integrated crop management (ICM) modules for 5 years in a maize-wheat rotation (MWR); wherein, ICM1&2-ˈbusiness-as-usualˈ (conventional flatbed maize and wheat, ICM3&4-conventional raised bed (CTRB) maize and wheat without residues, ICM5&6-conservation agriculture (CA)-based zero-till (ZT) flatbed maize and wheat with the residues, and ICM7&8- CA-based ZT raised bed maize and wheat with the residues. Results indicated that the ICM7&8 produced significantly (p < 0.05) the highest maize grain yield (5 years av.) which was 7.8–21.3% greater than the ICM1-6. However, across years, the ICM5-8 gave a statistically similar wheat grain yield and was 8.4–11.5% greater than the ICM1-4. Similarly, the CA-based residue retained ICM5-8 modules had given 9.5–14.3% (5 years av.) greater system yields in terms of maize grain equivalents (MGEY) over the residue removed CT-based ICM1&4. System water productivity (SWP) was the highest with ICM5-8, being 10.3–17.8% higher than the ICM1-4. Nevertheless, the highest water use (TWU) was recorded in the CT flatbed (ICM1&2), ~ 7% more than the raised bed and ZT planted crops with or without the residues (ICM4-8). Furthermore, the ICM1-4 had produced 9.54% greater variable production costs compared to the ICM5-8, whereas, the ICM5-8 gave 24.3–27.4% additional returns than the ICM1-4. Also, different ICM modules caused significant (p < 0.05) impacts on the soil properties, such as organic carbon (SOC), microbial biomass carbon (SMBC), dehydrogenase (SDH), alkaline phosphatase (SAP), and urease (URE) activities. In 0.0–0.15 m soil profile, residue retained CA-based (ICM5-8) modules registered a 7.1–14.3% greater SOC and 10.2–17.3% SMBC than the ICM1-4. The sustainable yield index (SYI) of MWR was 13.4–18.6% greater under the ICM7&8 compared to the ICM1-4. Hence, this study concludes that the adoption of the CA-based residue retained ICMs in the MWR could sustain the crop yields, enhance farm profits, save water and improve soil properties of the north-western plans of India.