Microbiome plays a crucial role in influencing the health and function of living beings as well as in regulating the biogeochemical cycles. The plant microbiome, in particular, has garnered significant research interest aimed at exploring the microbes that play a crucial role in regulating plant growth and nutrient acquisition. Recent advancements in omics sciences have played a crucial role in uncovering the complexities of these relationships. While techniques such as amplicon and shotgun metagenomics provide taxonomic profiling up to the species level and even the strain level, metatranscriptomics further elucidates the functional roles of these microbes. These techniques are being rapidly and widely adopted to understand the influence of microbes on the host. However, the challenge lies in their integration. Most studies to date rely on only one of these techniques, which limits the scope of holistic understanding of host-microbe interactions. Additionally, there is currently no well-established workflow that effectively combines these techniques to provide comprehensive biological insights. In this work, we describe an integrated approach for microbiome data analysis to provide biologically meaningful insights.