A field experiment was conducted during the Kharif and Rabi seasons of 2020-21 and 2021-22 at the Norman E. Borlaug Crop Research Centre, G.B.P.U.A & T., Pantnagar. Randomized block design was followed with 11 treatments and 3 replications. The main objective was to assess the influence of fertilizer and farmyard manure application, with or without Azotobacter and zinc, on crop yield and soil properties in a maize-wheat crop rotation. The data demonstrated that application of 100% RDF + FYM 5 t ha-1, resulted in a significantly higher system yield of 12,137 kg ha-1. Intercropping of cowpea with maize along with the application of FYM 10 t ha-1 showed the lowest bulk density in both surface (1.38 Mg m-3) and sub-surface (1.49 Mg m-3) soil and also it led to a reduction in the soil pH and EC. Additionally, hydraulic conductivity was higher in organic treatments, specifically in T6. However, the application of 100% RDF + FYM 5 t ha-1 resulted in the maximum retention of organic carbon (1.06% and 0.71%) as well as higher content of available nitrogen (185.11 and 175.95 kg ha-1), phosphorus (36.17 and 31.65 kg ha-1) and potassium (147.90 and 120.68kg ha-1) in surface and subsurface soil, respectively. The study suggests that the application of 100% RDF + FYM 5 t ha-1 contributes to improved soil fertility and sustainable crop yields.