The in-situ management of rice straw incorporation has become an essential practice in the rice–wheat cropping system with the growing adoption of super-seeder among farmers. While this equipment facilitates straw incorporation, nutrient immobilization from organic residues during decomposition poses a challenge to production. This study investigates the effect of bio-decomposer, nitrogen (N) level, and N scheduling on on various parameters in super-seeder sown wheat over two consecutive years (2020–21 and 2021–22). The experiment was laid in split-split-plot design without (B0) and with (B1) bio-decomposer, two nitrogen levels 150 (N1) and 180 (N2) kg ha−1 and three N splits (%) viz., 50: 25:25 (S1), 40: 30: 30 (S2), and 30:35:35 (S3) and replicated thrice. Results indicate significantly higher N concentration and uptake at pre- and post-anthesis with N2 and S1 compared to N1, S2, and S3. Post-anthesis N accumulation (post-NA) and remobilization (NR) were notably higher with N2. Dry matter accumulation (DMA) at anthesis and harvest significantly increased with N2 and S1 compared to N1 and S3, leading to significantly improved grain yield by 8.3% and 10.9% (two years mean). Soil urease activity (UA) significantly increased with bio-decomposer, N2, and S1 compared to B0, N1, and S3 at 30 and 60 DAS. Moreover, bio-decomposer enhanced soil microbial biomass carbon (SMBC). These findings underscore the importance of higher N levels with a greater basal N proportion in mitigating N stress and promoting sustainable wheat productivity. It also highlight the significance of effectively utilizing and conserving rice residue in the rice–wheat system.