The rhizosphere constitutes a crucial area where intricate interactions between plants and soil microbes unfold, not only influencing soil fertility but also impacting plant growth and productivity. It is widely acknowledged that a diverse array of soil microbes plays a crucial role in supporting the host plant. This encompasses nutrient provision, pathogen suppression, and the enhancement of tolerance against abiotic stresses. The rhizosphere is a complex habitat, containing millions of cells and thousands of microbes, making it one large genetic reservoir that holds the key to plant health. However, not all of the genes present within the rhizosphere are actively expressed. To truly understand the intricacies of interactions between plants and associated microbes, delving into the RNA through meta transcriptomics is essential. The approach will not only assist in comprehending the interactions between plants and specific microbes but also shed light on how the dynamics of microbial communities in the rhizosphere impact plant growth and productivity. It is also advantageous to identify the key taxa in the rhizosphere and understand the important ecological functions they perform. In this chapter, we concentrate on outlining the protocol for conducting a meta transcriptomic analysis to thoroughly investigate the interaction between plants and microbes in the rhizosphere. This encompasses the entire process from sample collection to data analysis. The data generated can be harnessed to develop effective agricultural strategies, such as optimizing plant growth through the utilization of beneficial microbes.