The degradation of soil quality in intensive cropping systems demands urgent attention to preserve soil health and sustain crop productivity. A 2‐year field experiment conducted in the loamy sand soil of Gujarat's Plains and Hills explored integrated nutrient management (INM) effects on nutrient dynamics, soil attributes, and microbial populations in maize (Zea mays L.)–sesame (Sesamum indicum L.) cropping. Using a randomized block design with three replications and 12 treatments, notable enhancements in soil physical conditions were observed following the integrated application of organic manure and inorganic fertilizers. Specifically, the application of 75% recommended dose of fertilizer (RDF) and 25% recommended dose of nutrient (RDN) through vermicompost, added with an NPK consortium via soil application, significantly increased N, P, and K uptake in the maize crop as compared with other treatments. The application of 75% RDF and 25% RDN through farmyard manure, added with an NPK consortium via soil application, led to a substantial increase of organic carbon levels and nitrogen availability in the soil post‐maize and sesame harvests, as well as with a marked increase in soil microbial populations. Correlation analysis representing the degree of association among all the traits underscores the potential of INM strategies to mitigate soil quality degradation and enhance nutrient cycling within maize–sesame cropping systems, thereby promoting agricultural sustainability in this specific agro‐climatic region.