<p>Rice-wheat system is a significant system for food production which generates a substantial amount of rice residues. Burning is a major challenge in Punjab and Haryana states of India that causes air pollution and greenhouse gases emission. The present investigation was aimed to identify the microbes and their potential for faster decomposition of rice residue with recommended rate of synthetic fertilizers for sustainably enhancing PAU Happy Seeder sown wheat production. The experimental findings revealed that generally 150&#xa0;kg N ha^− 1 (25% through farm yard manure and 75% through urea) (N₆) with microbial spray of consortia (<i>Aspergillus</i> sp. + <i>Delftia</i> sp.) (M₄) on in-situ rice residue after paddy harvest increased microbial viable cell counts <i>i.e.</i> total aerobic bacterial population (BP), fungal population (FP) and cellulose degrading bacteria population (CDBP), analysed using Scanning Electron Microscope (SEM) and Fourier Transform Infrared (FTIR) spectroscopy. The enrichment of microbial population led to better decomposition process of paddy straw that might have resulted to higher wheat productivity. Application of 150&#xa0;kg N ha^− 1 along with 3% urea spray (N₅) resulted in substantial yield increase from 9.1 to 17.2% over 120&#xa0;kg N ha^− 1 (recommended dose of fertilizer - RDF) (N₂) at Punjab Agricultural University, Ludhiana and University Seed Farm, Ladhowal. The interaction of N₆M₄ often producing the highest values and significantly influenced microbial viable cell counts at specific growth stages at both the location. The first principal component (Dim1) explains a major proportion of the variance (84.2 to 95.9%), while the second component (Dim2) contributes a smaller proportion (2.8 to 8.3%) indicating that Dim1 depicting the strong relationships among BP, FP and CDBP. Hence, <i>Delftia</i> sp. under N @150 kg ha^− 1 regime increased the succeeding wheat yield and effectively faster decomposition of rice residue.</p>