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Sporadic burning of rice straw and the particulate air pollution caused consequently have created a pressing need for identification of practical environmentally sound in situ rice residue management methods. However, the agronomic interventions associated with the agri-inputs particularly the type of nitrogen fertilizer source must be worked out for these interventions. In a two-year field study performed at two different locations representing sandy loam and clay loam soil types, zero tillage with application of nitrophosphate (applied as basal dose through drilling) in combination with urea (applied at 1st irrigation + 3 foliar sprays of urea at weekly interval) significantly enhanced the grain and straw yield of wheat. The soil microbial viable cell counts and dehydrogenase and urease enzyme activities were also recorded to be highest in this treatment indicating the occurrence of higher living microbial population. The treatment × response variable Principle component analysis (PCA) biplot depicted relative variation among the residue management treatments/Nitrogen fertilizer sub-treatments and the enzyme activities as response variables. A variation in the soil organic content components was recognized through Fourier transform infra-red spectroscopy (FT-IRS) studies. Irrespective of the soil types under study, the FT-IR spectra exhibited presence of the aromatic carbon functional groups in residue incorporated treatments as compared to the no residue incorporation treatment.