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Not AvailableLong term fertilizer experiment continues to act as the hotspot for studying the role of microbial interaction in nutrient supplying capacity. Despite plenty of studies, we have limited perception about the response of soil microorganisms to the long term application of fertilizer and manure. Hence, the present study was undertaken with the following treatments: no fertilizer and manure application i.e. control, 100% N (imbalanced fertilizer application), 100% NP (imbalanced fertilizer application), 100% NPK (balanced fertilizer application), 100% NPK+farmyard manure (FYM) at 5 t ha−1 (Integrated nutrient management; INM). The INM treatment had a significant build-up of total organic carbon (TOC), total N (TN) as compared to imbalanced fertilizer application and control. Similarly, INM also had significantly higher N mineralization potential and nitrification potential as compared to control and 100% N treatment. Heterotrophic nitrification rather autotrophic nitrification caused significant difference among different treatments. Microbial biomass and extracellular N cycling enzymes were also promoted substantially in INM. Discriminant function analysis with phospho lipid fatty acid (PLFA) biomarkers had produced arbuscular mycorrhizal fungi (AMF) and eukaryote as an important discriminant biomarker that cumulatively contributed 99.3% of total variations among the treatments and could have differentiated the control, imbalanced fertilizer application from balanced fertilizer application, and INM. Multiple regression showed that the TOC and protease activity are the key regulator of nitrogen (N) mineralization process and path analysis revealed that the NH4+-N followed by TOC, Microbial biomass is the important controller of Geometric mean of enzyme activities (GMea).ICA