Cotton-wheat rotation is one of the profitable cropping systems under arid climatic conditions in the agro-ecosystem of Punjab, Pakistan. The cropping system’s productivity factor is decreasing and is considered primarily due to imbalanced and non-integrated use of nutrients without taking care of soil health measures. Exploring the role of integrated site-specific nutrient management plans, treatments containing 2 fertilizer doses, and 3 management techniques on soil organic matter (SOM), soil P & soil K were studied in the cotton-wheat system of Punjab Pakistan for six crop seasons on a permanent layout. Substantial increase of 54-70% in SOM over the initial level of 5.0 g Kg^-1 in sandy loam soil was observed by adapting integrated nutrients management (INM) techniques. Similarly, significantly improved level of soil test phosphorus STP was observed at the end of the sixth crop season and INM techniques resulted in a 429% to 453% increase in STP. However, statistical analysis revealed a non-significant effect of doses, and a significant declining effect on soil K was observed with the applied technique of only mineral fertilizer application. Highly negative K balance suggests that the system will not be able to sustain the long-term supply of K. Ranking of indices from the best to the least favorable was recorded as P>SOM>K.